2024-04-22-final_Comm_Order.pdf

Findings of Fact and Order Little Rock Creek Sustainable Diversion Limit and Water Use Conflict

Morrison and Benton Counties

DATE: April 22, 2024

Names of Reviewers: Jason Moeckel and Randall Doneen, Section Managers, Dan Lais Central Region Manager, Division of Ecological and Water Resources, Minnesota Department of Natural Resources and staff.

Decision: The Commissioner has determined that authorized water use in the Little Rock Creek Area (as defined in the publication The Sustainable Use of Groundwater in the Little Rock Creek Area: A DNR Action Plan, September 2018) (2018 DNR Action Plan) is having a negative impact on the Little Rock Creek stream ecosystem in violation of the sustainability standard and other provisions of Minnesota Statutes section 103G.287. The Commissioner finds that a water use conflict exists among third priority water users in the Zone of Irrigation Influence (QBAA1 Zone of Irrigation Influence on Figure 1 below) for Little Rock Creek.

The Commissioner therefore establishes the sustainable diversion limit at 15% of the August median base flow to prevent the negative impact to Little Rock Creek described herein. The 15% of August median base flow is 0.8 cubic feet per second at station H15029003, 1.1 cubic feet per second at station H15029001, and 2.9 cubic feet per second at station H1503100.

The Commissioner will withhold consideration of new irrigation permits or increases in authorized volumes for third priority water use within the Zone of Irrigation Influence until the Commissioner approves a plan for the allocation of water among the third priority water users.

FACTUAL FINDINGS

Based on the information in the administrative record and the files with the Minnesota Department of Natural Resources (DNR) and consideration of the applicable laws, the DNR finds that there is substantial evidence in the record supporting that groundwater use in the Little Rock Creek Area is having a negative impact on Little Rock Creek; that it is necessary to establish a sustainable diversion limit to protect the stream ecosystem; and that a water use conflict exists among third priority water users in the Little Rock Creek Area.

Background and Location

1. Little Rock Creek is located at the boundary of Benton and Morrison Counties in central Minnesota. The nearest cities are Rice and Royalton. Little Rock Creek originates in Morrison County, flows west, then generally southward into Benton County and Little Rock Lake and ultimately discharges to the Mississippi River via the Harris Channel at Mississippi River mile

937. Its main tributary is Bunker Hill Brook (commonly referred to as Bunker Hill Creek) which joins Little Rock Creek approximately 1.2 miles north of Little Rock Lake. Little Rock Creek is

1 Quaternary Buried Artesian Aquifer (QBAA) is the buried sand aquifer in this area.

Morrison and Benton Counties located in numerous sections of Morrison and Benton Counties within Townships 38N and 39N, and Ranges 30W and 31W. Little Rock Creek and Bunker Hill Creek are public waters within the meaning of Minn. Stat. § 103G.005, subd. 15. Little Rock Creek’s Public Waters Inventory (PWI) identification number is 05003a. Bunker Hill Creek’s PWI identification number is 05004a.

2. Little Rock Creek is approximately 23.8 miles in length and its watershed is 44,229 acres, divided between Benton County (12,590 acres) and Morrison County (31,639 acres). The mainstream segment is perennial, whereas a majority of the tributaries to the creek are either intermittent or have been excavated to function as drainage ditches.

3. Segments of Little Rock Creek and its tributary, Bunker Hill Creek, are designated trout streams as listed in Minnesota Rule 6264.0050 Subpart 4(D). These trout streams are designated as Special Management Waters as described in Minn. Stat. § 97C.005 subd. 1(2). The Little Rock Creek trout stream segment is 21.7 miles long and is managed for trout, but many other aquatic species thrive in the creek including native species adapted to cold water streams.

The Bunker Hill Creek designated trout stream segment is similarly managed, has similar aquatic species, and is 4.7 miles long. Descriptions of the locations of, and restrictions on, designated trout streams can be found in Minnesota Rule 6264.0050.

4. Little Rock Creek and Bunker Hill Creek are unique bodies of water in Central Minnesota as they are cold water streams. The streams contain a diverse fish community with 28 species sampled in 1992. The most common species include White Sucker, Blacknose Dace, Johnny Darter, and Creek Chub (Barr Engineering, Little Rock Creek Watershed Total Maximum Daily Load Report: Dissolved Oxygen, Nitrate, Temperature and Fish Bioassessment Impairments 2015). Little Rock Creek was originally stocked with Brown Trout in 1908. Yearly stocking occurred from 1962 to 1972. Stocking resumed in 1995. Brown Trout was the primary species stocked while Brook Trout were used periodically. In 2022, the DNR stocked Brook Trout and intends to continue stocking Brook Trout, based on availability. The DNR and the Minnesota Pollution Control Agency (MPCA) periodically conduct trout population assessments, fish community assessments, and stream temperature monitoring.

5. Riparian landowners and other members of the public use Little Rock Creek for angling, hunting, and passive recreation. Two segments of Little Rock Creek are sites of DNR administered Aquatic Management Areas (AMA). These AMAs are “access easements” acquired by the State of Minnesota on private land in and along the stream that provide for public angling and DNR stream habitat management. In addition, two Wildlife Management Areas (WMA) adjacent to the creek provide public hunting and passive recreation as well as DNR wildlife habitat management. Little Rock Creek passes through the Sartell WMA which contains an impoundment of Little Rock Creek that can be managed to provide waterfowl habitat.

6. Little Rock Creek overlays a water-table aquifer and a system of buried, unconsolidated aquifers and leaky aquitards (geologic bodies that transmit water at a slow rate).

Morrison and Benton Counties

Little Rock Creek and its tributaries are fed by the water-table aquifer. The water-table aquifer is influenced by the underlying and adjacent buried aquifers and leaky aquitards. See generally, DNR, Groundwater Flow and Groundwater / Stream Interaction in the Little Rock Creek Area, 2021 and references therein.

7. The Cities of Rice, Royalton, and Buckman pump groundwater from wells in the Little Rock Creek Area to provide water for approximately 4,000 residents (U.S. Census Bureau, 2010). Only the City of Rice has wells located within the Zone of Influence, and these wells are on the downstream edge of the zone. Approximately 1,650 residents live in the countryside and get their domestic water from private wells. Per state statute, both the City of Rice and rural residents are first priority users, to the extent that such water is used for domestic water supply.

The needs of the domestic water supply must be satisfied before agricultural irrigation, which is a third priority use, and therefore DNR does not consider these first priority users to be part of the water use conflict. The City of Rice also has second priority, third priority, fifth priority and sixth priority water use. Any plan approved by or ordered by the DNR will need to account for these fifth and sixth priority uses for those uses to continue. See Minn. Stat. § 103G.261 (setting forth the six priority levels for water allocation).

8. Groundwater appropriation permits that currently exist in the Zone of Influence of Little Rock Creek Area include permits for agricultural irrigation (91 permits), livestock watering (one permit), municipal/public water supply (one permit), and nursery irrigation (one permit). The municipal/public water supply category consists of domestic use and other, lower priority uses.

9. Currently, there are no water appropriation permits authorizing direct withdrawal of water from Little Rock Creek. However, between 1969 and December of 2022 the DNR has issued 94 groundwater appropriation permits, for 3.7 billion gallons (“BG”) of water, used mainly for irrigation of about 12,000 acres within the Little Rock Creek Zone of Influence. Actual water use fluctuates largely dependent on rainfall.

10. There are currently four stream gages in Little Rock Creek that collect year-round stage, discharge, and water temperature data every 15 minutes. Two sites on Little Rock Creek, H15029001 (Long Term Gauge) and H15031001 (Downstream Gauge), have continuous records that date back to 2007. The DNR’s long term gaging station (H15029001) is in Benton County, in the NW1/4 of the NW1/4, Section 10, Township 38N, Range 31W, approximately 0.23 miles north of the confluence of Little Rock Creek and Bunker Hill Brook (see Figure 1). In mid-2014, the DNR installed stream gages on two additional sites on Little Rock Creek. In addition to the four stream gages (only three will be used for evaluation), the DNR measures discharge at six locations along the creek periodically throughout the year. There are also periodic discharge measurements in the DNR files for Little Rock Creek dating back to 1969. There are two monitoring locations on

Morrison and Benton Counties

Bunker Hill Creek, only one is a continuous stream gage intermittently operated by the MPCA since 2006.

11. In 2015 the MPCA published the Total Maximum Daily Load (TMDL) Report for Little Rock Creek. The TMDL report is based in part on the 2009 Benton Soil and Water Conservation District’s (SWCD) Stressor Identification Report. Below are key excerpts from the TMDL report that relate directly to the actions in this Commissioner’s Order. According to the TMDL report:

“The Little Rock Creek Stressor Identification report (Benton SWCD, 2009) cites lower groundwater levels as a possible contributor to the impairments for dissolved oxygen and temperature. The data show that the dry weather and associated low flow conditions from the TMDL monitoring period (2006 through 2008) were not as severe as the 1988 drought, but the persistence of dry conditions resulted in above average pumping rates for agricultural irrigation (normalized to the drought index) for six consecutive years that may have exacerbated the flow conditions for Little Rock Creek”.

"The ideal combination of implementation strategies, or combinations of Best Management Practices (BMPs), would provide some or all of the following:

• Reductions in groundwater use will be necessary to improve conditions in the stream.

A variety of potential options to reduce groundwater use should be explored, including: limits on total appropriations, improved irrigation efficiency, scheduling and technologies, identifying alternative sources, timing, proximity to the stream and other options not yet identified

• Nutrient and organic constituent reductions

• Creating more of a free-flowing system, while incorporating current (Sartell) Wildlife

Management Area (WMA) management strategies, to improve connectivity and temperature issues during the critical conditions described in this report."

12. In 2016, DNR invited potentially affected stakeholders in the Little Rock Creek Area to share, learn, and consult with DNR to develop the 2018 DNR Action Plan. The DNR assembled and consulted with a 28-member advisory team to inform a groundwater management plan written by the DNR for the Little Rock Creek Area. The majority of the advisory team members were individuals that held water use permits in the Little Rock Creek Area. The DNR convened the advisory team 14 times to provide information about the DNR’s responsibilities and to solicit stakeholder advice. The DNR also held a public, open house meeting on December 19, 2017, before finalizing the 2018 DNR Action Plan.

13. Since the plan was finalized, the DNR has held seven public meetings to update interested parties. The stakeholder meetings provided an opportunity for updates on progress implementing the plan, discussion of technical and regulatory questions, and sharing opinions

Morrison and Benton Counties and perspectives about groundwater issues. Actions recommended by the plan include development of a groundwater flow model, which would be used in establishing a protected flow and determining a sustainable diversion limit. This Commissioner’s Order addresses several recommendations of the Plan, but one recommendation is not addressed due to a statutory change. Due to revisions to Minn. Stat. § 103G.287, subd. 2, the DNR is no longer required to set a protected flow for Little Rock Creek. The DNR is instead setting a sustainable diversion limit as authorized by this statute.

14. The DNR also convened a Technical Advisory Group (TAG) during the development of the DNR’s groundwater flow model. The TAG included technical staff from various governmental entities such as the Minnesota Department of Health, Minnesota Department of Agriculture, MPCA, United States Geological Survey and several environmental and engineering consulting firms. The TAG reviewed the suitability of the numerical model to predict the effect of groundwater appropriation(s) on groundwater flows and contributions of groundwater flows to base flow2 to Little Rock Creek. The TAG members provided comments and feedback on a draft modeling report in January 2019. There was general agreement among the members of the TAG that the DNR’s technical approach was suitable for the purpose of calculating cumulative stream flow diversion associated with groundwater appropriations.

15. At the stakeholder meetings, the DNR invited public feedback relating to each of the following topics that are addressed in this Commissioner’s Order:

• Limiting streamflow diversions to 15% of the August median base flow at each of three gauges. This is described as the sustainable diversion limit.

• Declaring a water use conflict (Minn. Rules Chapter 6115.0740).

• Establishing a temporary moratorium on new irrigation permits and increases in authorized volumes of irrigation permits within the Zone of Irrigation Influence.

16. DNR had considered including a “temporary just cause exemption” from the application of Minn. Stat. § 103G.285 in this Commissioner’s Order. The exemption is no longer necessary because Minn. Stat. § 103G.287, subd. 2 no longer requires compliance with Minn.

Stat. § 103G.285 if groundwater appropriations are causing negative impacts to surface waters.

In particular, groundwater appropriations with negative impacts on surface waters no longer trigger the requirement in Minn. Stat. § 103G.285, subd. 5 to limit appropriations from trout streams to temporary appropriations. The DNR presented information on the proposed Commissioner’s Order at a March 16, 2023, stakeholder meeting, a GovDelivery notice to 4,779 recipients on March 27, 2023, and a notice on the project webpage. The public was invited to send a response to the DNR via email.

2 Base flow represents an estimate of stream flow in the absence of direct runoff, largely sustained by groundwater discharges.

Morrison and Benton Counties

17. Below is a brief overview of the stakeholder feedback on each part of the proposed order. A complete copy of the stakeholder feedback is attached as Exhibit A, and DNR’s Response to Stakeholder Feedback is attached as Exhibit A.

• Limit streamflow diversions to 15% of the August median base flow at each of three gauges.

Respondents suggested that the 15% of the August median base flow diversion limit determined by DNR was arbitrary and recommended 20% of the August median base flow. Some respondents were skeptical of the DNR’s technical analysis and believed it was unreliable due to the assumptions made, the short period of record for monitoring data, and the fact that water users overreported their water use. Some respondents disagreed with the DNR’s decision to use dryland alfalfa as a “no irrigation” alternative scenario. Some recommended comparing present groundwater diversion to a landscape dominated by native vegetation.

• Declare a water use conflict.

Respondents suggest that the water use conflict should be resolved by augmenting stream flow with well water. Some respondents are concerned that any decision to reduce water availability for irrigation will create damage to local economies. Some respondents believe that piping water from a distance (to supplant irrigation water) is too expensive, complicated, and unnecessary in years where rainfall is high. Some respondents believe that the Zone of Irrigation Influence is arbitrary, too wide and contradicted by hydrologic studies in other regions of the United States.

• Declare a temporary moratorium on new permits and increases in authorized volumes within the Zone of Irrigation Influence.

No comments were received.

Water Quality

18. Water quality in Little Rock Creek is impaired. The Benton Soil and Water Conservation District published in September of 2009 (and revised in February of 2010) the “Little Rock Creek Stressor Identification Report” (2009 Stressor ID). This report evaluated 37 potential stressors of water quality in Little Rock Creek. Seven main stressors were identified for Little Rock Creek. In order of priority, they are: 1. Flow alteration, 2. Temperature, 3. Sediment – deposited and bedded, 4. Nitrates (toxin)/Ammonia, 5. Dissolved oxygen/Biological Oxygen Demand, 6.

Connectivity, 7. Predation of trout by pike and other warmwater piscivores. The report cites lower groundwater levels as a possible contributor to the impairments for dissolved oxygen and temperature. The report recommends documenting any relationship between increased irrigation and lower groundwater levels. Barr Engineering then completed the report entitled Little Rock Creek Watershed Total Maximum Daily Load Report: Dissolved Oxygen, Nitrate, Temperature and Fish Bioassessment Impairments (TMDL) 2015, which was submitted to the Environmental Protection Agency by the MPCA. The TMDL report also cites lower groundwater levels as a possible contributor to the impairments for dissolved oxygen and temperature.

Morrison and Benton Counties

Technical Findings

Hydrogeology and Groundwater Flow Analysis

19. To determine the sustainable diversion limit [Minn. Stat. § 103G.287, subd. 2] for Little Rock Creek, the DNR considered factors identified in, and the general process set out in the DNR’s Report to the Minnesota State Legislature (DNR, Definitions and Thresholds for Negative Impacts to Surface Water, January 2016). The process laid out in the thresholds report was the outcome of a 2015 legislative requirement directing the DNR to develop recommendations for the calculation of thresholds for negative impacts to surface waters. This process for determining a sustainable diversion limit for natural watercourses was reviewed by aquatic resource experts both internal to and external to the DNR, including aquatic resource professionals from the U.S.

Geological Survey (USGS), and the University of Minnesota.

20. As described above, the following protocol were used to determine a sustainable diversion limit:

• Develop a Water Budget: DNR used industry standard groundwater and surface models to calculate a water budget for Little Rock Creek that accounts for all water inflows into and water losses from the stream. The models are MODFLOW (Modular three-dimensional finite-difference ground-water flow model) and GSSHA (Gridded Surface Subsurface Hydrologic Analysis).

• Determine Characteristic Streamflow: DNR examined historic water level records for Little Rock Creek and evaluated the characteristic stream flows to determine the variability and range of flows that are necessary for maintaining the stream’s hydrology, ecology (including fish and wildlife habitat) and in-stream uses3.

• Determine the August Median Base Flow: DNR used established techniques in the field of hydrology to combine modeled streamflow diversions with the observed flow record, to calculate the August base flow from the resulting flow record, and to compute the median values.

3 An in-stream use is a use made of any water body in its natural condition by natural systems, the public at large, and riparian landowners that is dependent upon maintaining sufficient water in the water body to support such uses, including recreational uses such as swimming, boating, sport fishery habitat, and skating as well as water quality, aesthetics, and electrical power generation. See e.g., Mathew Levinson, California Water: An Economic Consideration, 12 UCLA J. of Envl. Law & Policy 183, 185 (1993); Lawrence J. MacDonnell, Federal Interests in Western Water Resources: Conflict and Accommodation, 29 Nat. Resources J. 389, 408-09 (1989); National Audubon Society

v. Superior Court, 658 P.2d 709, 725-26 (Cal. 1983) (defining in-stream uses to include navigation, fishing, recreation, ecology, and aesthetics).

• Assess Appropriation Impact: DNR used the groundwater models to assess how much water existing appropriations are diverting from the system, and how those diversions might affect the stream’s hydrology.

• Determine Change and Abundance of Fish Habitats Due to Groundwater Withdrawal: DNR completed an instream flow habitat characterization and analysis to calculate the loss of habitat under various low flow scenarios and establish a relationship between habitat loss and reduction in streamflow. The predicted loss in habitat is used to determine a likely change in the biological community and ecology in a manner that results in a less desirable and degraded condition, and therefore, ecosystem harm.

• Determine the Effect of Streamflow on Water Temperature: DNR completed a water temperature and streamflow analysis using dye trace techniques to evaluate time of travel, analyze temperature data from multiple stream locations over many years, and evaluate changes due to an impoundment and streamflow depletion.

21. As described in Champion, The Evaluation of Conceptual Groundwater-use Management Actions, Little Rock Creek Area, August 2022, the DNR used the MODFLOW model to delineate a zone of irrigation influence around Little Rock Creek. The DNR delineated a zone for the buried aquifer system (QBAA Zone of Irrigation Influence) and a separate zone for the water table aquifer (QWTA Zone of Irrigation Influence). (The term “Zone of Irrigation Influence” refers to the QBAA Zone of Irrigation Influence.) To better reflect the precision of the information and to make the boundaries more easily recognized on the ground, the zones of irrigation influence were delineated using quarter-quarter section increments. Figure 1 displays the zones of irrigation influence and the capture modeling data points used to delineate these zones. The aquifers may be thin or absent in some areas within each zone. Irrigation wells located outside of the relevant zone of irrigation influence are expected to have negligible or positive influence on base flows in Little Rock Creek at the three evaluation stations (upstream, long-term, and downstream).

https://files.dnr.state.mn.us/waters/groundwater_section/sustainability/littlerock/lrca-concept-evaluations-report.pdf https://files.dnr.state.mn.us/waters/groundwater_section/sustainability/littlerock/lrca-concept-evaluations-report.pdf

Figure1– “Groundwater Flow and Groundwater / Stream Interaction in the Little Rock Creek Area” MN DNR, 3-4-21

22. Stream flow and temperature data, observation-well data, and groundwater mapping provide substantial evidence of a direct relationship between groundwater and Little Rock Creek, including Bunker Hill Creek. The perennial flows measured in Little Rock Creek and Bunker Hill Creek support the finding that groundwater is a source of streamflow in both creeks.

The relatively cool temperatures measured in Little Rock Creek under base-flow conditions during the summer months also demonstrate that groundwater is a major source of base flow. Data collected in observation wells located near Little Rock Creek show that the elevation of the water table is above the elevation of the nearby stream channel. Mapping of the water-table and buried-aquifer potentiometric heads shows that groundwater flows toward Little Rock Creek and other streams which contributes to baseflow (DNR, Benton County Part B Atlas, plate 6 and plate 8, 2012 and Morrison County Part B Atlas report, 2019).

23. Aquifer-test and observation-well data demonstrate that buried aquifers are connected to the water-table aquifer and, therefore, connected to Little Rock Creek and other surface waters. Aquifer tests performed on irrigation wells by DNR staff, in cooperation with the well owners, demonstrate that confining geologic barriers between aquifers are leaky, and pumping drawdown radiates rapidly to adjacent aquifers not screened in the pumping well, including the water-table aquifer. Nests of closely spaced observation wells screened at different depths show that, in most locations, the elevation of the water table is above the elevation of the potentiometric surface in underlying buried aquifers. This indicates that at these locations, there is a downward component to flow from the water table aquifer toward underlying, buried aquifers. In two observation-well nests located near Little Rock Creek, this relationship is reversed during ambient flow conditions. This indicates that at these locations near Little Rock Creek, groundwater leaks upward from buried aquifers toward the water table. Taken together, these facts demonstrate that buried aquifers in the area, including aquifers that are the source for water appropriation permits, are hydrologically connected to the water-table aquifer and to Little Rock Creek, including Bunker Hill Creek.

24. Groundwater pumping can reduce streamflow by decreasing groundwater discharge to streams and, in some cases, by inducing or increasing seepage out of streams.

Irrigation and associated irrigated crops are land uses directly related to groundwater appropriations that can substantially affect the amount and timing of groundwater discharge to streams.

25. The continuous stream gaging record for Little Rock Creek only includes years with significant groundwater use. To assess the impacts of groundwater appropriations on streamflow, it was necessary to estimate streamflow and base flow characteristics for a reference condition using a paired watershed study. The DNR used the Rice Creek watershed, 25 miles to the southeast of Little Rock Creek that has substantially less permitted groundwater use. The Rice Creek Watershed shares many similarities, including size, climate, correlation between daily discharge values, and the existence of stream gage data.

26. The DNR completed its streamflow analysis at the long-term gage (H15029001) with continuous flow measurements in 2006, and 2008 through 2018, and periodic measurements dating back to 1978. Streamflow in Little Rock Creek follows a typical pattern in Minnesota with the highest flows measured in April, May, and June, and with summertime low flows typically in August.

27. The DNR used a commonly applied, automated method to separate base flow from total streamflow. The median August base flow at gage H15029001 during the analysis period of 2006 and 2008 through 2012 is 6.8 cubic feet per second (cfs). A full description of the base flow analysis is described in the DNR report Champion, Groundwater Flow and Groundwater / Stream Interaction in the Little Rock Creek Area, January 2021.

28. Streamflow data were extrapolated from H15029001 to upstream gage H15029003 in order to complete the habitat analysis. Prior to the beginning of continuous records at station H15029003 in July 2014, the stream gage record at station H15029003 was estimated using station H15029001 records.

29. The DNR developed a numerical, computer model of the Little Rock Creek Area hydrologic system (“LRCA model”) to estimate base flows under the reference condition and to provide a tool to evaluate base flow under potential management scenarios that may be considered. See Champion Groundwater Flow and Groundwater / Stream Interaction in the Little Rock Creek Area, January 2021. The DNR considered available data on groundwater use, climate, land use, soils, hydrology, and geology in developing the model. The baseline model computes groundwater heads and stream base flows representing March 2006 through September 2018.

The model reasonably matches observed monthly base flows outside of winter/ice-affected periods, particularly during summer low-flows, which is the focus of the evaluations using the model. As stated in paragraph 14 above, the Technical Advisory Group generally agreed that the DNR’s technical approach was suitable for the purpose of calculating cumulative stream flow diversion from groundwater use.

30. Numerical groundwater flow modeling provides additional evidence of a direct relationship of groundwater and Little Rock Creek, including Bunker Hill Creek. Therefore, pumping of groundwater from nearby permitted irrigation wells is diverting water from Little Rock Creek or intercepting groundwater that would be flowing to the creek.

31. The DNR calculated base-flow diversions as the difference between computed base flows (computed groundwater-sourced discharge) in Little Rock Creek during the modeling period versus computed base flows in a reference condition without groundwater pumping or use (no-use scenario). Base-flow diversions were calculated at three continuous stream-gaging locations.

32. In the no-use scenario model, there was no groundwater pumping, and irrigated crops were replaced with non-irrigated alfalfa. Non-irrigated land covers remained the same as the baseline. DNR selected a non-irrigated agricultural crop to replace irrigated crops in the no-use scenario to isolate the effects of groundwater appropriation in an agricultural setting. DNR does not propose reverting the agricultural landscape to pre-settlement land cover nor are there any local or regional plans calling for such a change. DNR selected alfalfa as a representative crop because water use by non-irrigated alfalfa is at the upper end of the range for non-irrigated, agricultural land uses in Central Minnesota (i.e., row crops, other hay crops, small grains, and pasture) and because alfalfa is more drought tolerant than many row crops.

33. The DNR calculated estimates of streamflow under the reference condition as the sum of the computed base-flow diversions and measured streamflow. Similarly, DNR calculated estimates of base flow under the reference condition as the sum of the computed base-flow

Morrison and Benton Counties diversions and base flows estimated directly from measured streamflow using a base-flow separation filter. This method of calculating the reference condition flows takes advantage of the best available data. The measured streamflow record and computed base flows overlap during 2006 and 2008 through September 2018, however, data were missing from the long-term gage for most of 2007.

34. The DNR assessed the sensitivity of computed base-flow diversions to key model assumptions, model parameters, and to the selected reference condition. The computed base-flow diversions were sensitive to changes in pumping volumes and the selected reference land cover but were relatively less sensitive to changes to model parameters, such as aquifer characteristics.

35. Considering the model and all other available evidence, the DNR concludes that monthly August base-flow diversions exceeded one cubic foot per second (cfs) in at least some years for the selected reference conditions during the analysis period (2006, 2008 through 2018) at the long-term stream gage (station 15029001). The reference August median base flow was determined to be 7.2 cfs at the long-term stream gaging station. The August monthly maximum diversion was calculated at 1.9 cfs (27%), and the August median diversion is 0.77 cfs (11%).

36. The DNR used the same methods to calculate reference-condition streamflow and base flow at the upstream gage (station 15029003) for input to the stream hydraulic model used in the stream habitat assessment. The reference August median base flow was approximately 5.5 cfs at the upstream gage. The August monthly maximum diversion was calculated at 1.4 cfs (25%), and the August median diversion is 0.64 cfs (12%).

37. The DNR used the same methods to calculate reference-condition streamflow and base flow at the downstream gage (station 15031001). The reference August median base flow was 19 cfs at the downstream gage. The August monthly maximum diversion was 5.0 cfs (26%), and the August median diversion was 2.3 cfs (12%).

38. The DNR conducted a water use calibration study by deploying acoustic flow meters on irrigation systems in the Little Rock Creek Area. Local landowners volunteered nine local irrigation systems for use in the calibration study during the 2018 and 2019 irrigation seasons. The DNR compared the “metered” versus reported average pumping rates for both years and total volumes for 2019 (Flow Meter Study Double blind study of calculated and reported water use in the Little Rock Creek Area 3/4/2021). Four of the systems had reported pumping rates within 10% of the measured values. Four of the systems had reported pumping rates that were more than 10 percent greater than the measured values and one system reported pumping rates that were more than 10% lower than measured values. The results suggest that reported irrigation volumes might be overestimated or underestimated depending on circumstances, methods, and age of systems.

39. To test the models’ sensitivity to the potential for systematic overestimating, the DNR developed a model run with groundwater uses modified to 80 percent of the reported volumes. The result was a computed reduction in the median base flow diversion of 0.27 cfs at station 15029001. This resulted in computed monthly maximum diversion of 21%, a difference of 6% compared to using the reported volumes as described in paragraph 35.

40. This water use calibration study included 9 of the 398 permitted wells in the Little Rock Creek Area and may not be broadly representative.

41. The DNR conducted an inter-watershed comparison as an independent line of evidence on the relationship between groundwater-use rates and summer base flow. DNR staff compared concurrent records of August base flows (2008 and 2009) in Little Rock Creek with base flow in a nearby watershed (Rice Creek) with similar characteristics but where there is substantially less groundwater use. Base-flow per square mile of watershed in Rice Creek for August 2008 and 2009 was 59% and 26% greater than base flow in Little Rock Creek. The model-computed base flow in the no-use scenario was 59% and 16% greater than in the baseline model for August 2008 and 2009.

Stream Habitat Analysis

42. The DNR used the Instream Flow Incremental Methodology (IFIM), which is a modular decision support system for assessing potential flow management schemes. The IFIM is designed to assist natural resource and water management agencies in comparing the relative habitat impacts of proposed instream flow management schemes with reference conditions. A unique feature of the IFIM is the simultaneous analysis of habitat variability over time and space, while incorporating data from streamflow gaging and groundwater modeling estimation of streamflow depletion from groundwater use.

43. The flow regime, as described by the hydrograph, is the key driver of aquatic ecosystems. All parts of the hydrograph are important. For example, high spring streamflow initiates and enables spawning, moderate flows clean substrates, and summer low flows provide habitat for growth and survival. In Little Rock Creek, groundwater pumping has the greatest effect during the low summer flows. August flows were the focus of the IFIM habitat analysis because this is a time of intense groundwater use; summer low flows are known to influence fish growth and survival, be and a limiting factor of fish abundance.

44. DNR’s groundwater model quantified the change in low flows during periods of pumping and without pumping (reference period). The reduction in reference flows by 25% or more of the August median base flow (“ABF”) (that is, reference flows of 75% or less of the ABF) is significant and intensifies as flows decrease. In four of the 12 years modeled, the August low flows were 35% lower and 40% more frequent with groundwater pumping.

45. Fish habitat preference criteria were developed using statewide samples and by sampling Little Rock Creek, at a study site just downstream from County Road 26, for fish and associated habitat. Microhabitat data were recorded at each sampling location, regardless of whether any fish were captured. Variables recorded with each sample included: river, site location, date, weather conditions, water and air temperature, conductivity, dissolved oxygen, sample location, gear type, three water depths, three mean column velocities, substrate types, and cover types.

46. Habitat preference values for all target species-life stages (juvenile or adult) were calculated for depth, velocity, and substrate and a habitat time series was created by merging the discharge – habitat relationship (i.e., merging specific species-life stage curves with a hydrologic time series).

47. At the current level of groundwater pumping (baseline condition in Figure 2), five of six habitat guilds lost significant (>20%) habitat as flows decreased. The habitat for all aquatic species inhabiting fast riffles, slow riffles, raceways, medium pools, and deep pools lost a significant quantity of habitat. Only shallow pool species are relatively unaffected by the decrease in low flows.

48. Scenarios of stream flow depletion and their impact on the Weighted Usable Area (WUA) of habitat guild representatives were developed, based on 5% increments of the August median base flow (e.g., 5% ABF, 10% ABF, 15% ABF).

Figure 2- Habitat / Flow Relationship in Little Rock Creek.

49. At a depletion level equivalent to the 20% of the ABF, four of six habitat guilds lost significant (>20%) habitat.

50. When stream depletion is limited to no more than 15 percent of the August median base flow (highlighted as abf15 in Figure 2), habitat loss remains below the 20 percent threshold except for one species-life stage (slow riffle habitat representative), which was marginally over the threshold (21% loss).

51. The DNR’s analysis shows that habitat loss for all species life stages is below the 20% threshold when stream depletion is limited to 10 percent of the August median base flow.

52. Low stream flows in Little Rock Creek are further reduced by groundwater pumping. Current pumping and use conditions reduced stream flows by more than 20% of the August median base flow in four of the 12 years of the period of record (2006, 2008-2018). The reduction in reference flow is significant and increases as flows decrease. The percent change between reference (without pumping) and baseline (with pumping) conditions was greater than 35% in low flow magnitude, frequency, duration, and recurrence. The impact of this reduction in flow corresponds to a significant loss of fish habitat. Five of six habitat guilds lose significant (>20%) habitat as flows decrease. Only shallow pool species are relatively unaffected by the decrease in low flows. Scientific literature reports that habitat loss and pollution are the primary causes of extirpation of aquatic biota in streams and rivers. On the basis of these findings and related scientific literature, the current magnitude of habitat loss during August across the majority of habitat types (5/6) equates to ecological harm. At current pumping volumes habitat loss in August due to groundwater pumping will likely alter the biological community and exceed the threshold for ecological harm (See Champion, The Evaluation of Conceptual Groundwater-use Management Actions, Little Rock Creek Area, August 2022).

Water Temperature Analysis

53. The Benton Soil and Water Conservation District published the Little Rock Creek Stressor Identification Report in September of 2009 and revised it in February of 2010. This report identified water temperature as one of the primary stressors present for a water quality impairment.

54. A 2015 report by Barr Engineering: Little Rock Creek Watershed Total Maximum Daily Load Report: Dissolved Oxygen, Nitrate, Temperature, and Fish Bioassessment Impairments (TMDL) cites the presence of the impoundment in the Sartell Wildlife Management Area (WMA) and lower groundwater levels as contributors to the impairment for temperature.

55. The DNR Division of Fish and Wildlife manages a dam and the impoundment at the Sartell WMA. The dam was installed in 1978. It is a sheet pile dam with a 48-foot-wide crest and a series of stop logs that are used to control water levels. When filled, the impoundment is a little over 20 acres in area with water depth ranging from 0.5 to 3 feet deep. When filled, the impoundment is more than 600 feet wide, which creates a large surface area for the water to warm from the sun. Periodically, the impoundment is drained to establish vegetation. During these drawdowns, the impoundment is drained and the flow of water in Little Rock Creek is largely confined to a meandering channel that is less than 60 feet wide.

56. Monitoring data shows that seasonal and daily water temperatures are distinctly warmer at sites that are downstream of the Sartell WMA impoundment. In the spring season, https://files.dnr.state.mn.us/waters/groundwater_section/sustainability/littlerock/lrca-concept-evaluations-report.pdf https://files.dnr.state.mn.us/waters/groundwater_section/sustainability/littlerock/lrca-concept-evaluations-report.pdf https://www.pca.state.mn.us/sites/default/files/wq-iw8-09e.pdf https://www.pca.state.mn.us/sites/default/files/wq-iw8-09e.pdf https://www.pca.state.mn.us/sites/default/files/wq-iw8-09e.pdf

Morrison and Benton Counties daily average temperatures for all sites vary by less than one degree Celsius, but as the summer progresses, daily average temperatures differ by more than three degrees Celsius between sites upstream of the impoundment where water is cooler and downstream of the impoundment where water is warmer.

57. Four time of travel studies were conducted on Little Rock Creek to quantify the differences in travel time and stream dynamics when the impoundment is in place as well as when the impoundment is removed. Under low flow conditions, removing the dam decreased travel time from an upstream site through the WMA from 48 hours to 32 hours. The amount of time that dye was present at the site downstream of the dam decreased from 26 hours with the dam in place to 14 hours with the dam removed.

58. The temperature increases observed downstream of the Sartell WMA are a result of the impoundment slowing travel times through the WMA by more than 10 hours under low flow conditions and greatly increasing surface area at the impoundment, both of which result in increased solar warming in the WMA and downstream. The DNR has subsequently removed the stop logs at the impoundment on an experimental basis to evaluate the benefits of removing the impoundment and any potential impacts.

59. Water temperatures in Little Rock Creek above the impoundment exceeded the chronic water temperature standard most frequently in 2011, by more than 20 days at County Road 40 (upstream of the impoundment) and 40 days at County Road 26 (site farthest upstream of the impoundment), which is about twice as many days as any other year in the period of record. The impact of groundwater inflow on stream temperatures, however, is less clear.

Streamflow’s during the summer of 2011 represented some of the highest summer flows in the period of record, including the highest August base flows. At these higher flows, small changes in base flow due to groundwater withdrawal would be an insignificant factor in the water temperature exceedances. In contrast, 2012 experienced considerably lower flows during the month of August and above average groundwater pumping, and yet 2012 had some of the fewest exceedances of the chronic water temperature standard at the farthest upstream site (County Road 26). Our analysis did not establish a significant role for groundwater withdrawals in the temperature exceedances relative to the water temperature standard. However, it’s well documented in scientific literature that localized groundwater inflow can provide important pockets of cooler water and serve as refuge habitat during periods of high temperature.

Application of Statutes and Rules

60. Minn. Stat. § 103G.255 states that the Commissioner shall administer the use, allocation, and control of waters of the state.

61. Minn. Stat. § 103G.265, subd. 1 states that “the Commissioner shall develop and manage water resources to assure an adequate supply to meet long-range seasonal

Morrison and Benton Counties requirements for domestic, municipal, industrial, agricultural, fish and wildlife, recreational, power, navigation, and quality control purposes from waters of the state.”

62. Minn. Stat. § 103G.287, subd. 5 states that “The Commissioner may issue water-use permits for appropriation from groundwater only if the Commissioner determines that the groundwater use is sustainable to supply the needs of future generations and the proposed use will not harm ecosystems, degrade water, or reduce water levels beyond the reach of public water supply and private domestic wells…”

63. Minn. Stat. § 103G.287, subd. 3 provides that the Commissioner may establish water appropriation limits to protect groundwater resources. In doing so, the Commissioner must consider “the sustainability of the groundwater resource, including the current and projected water levels, cumulative withdrawal rates from the resource on a monthly or annual basis, water quality, whether the use protects ecosystems, and the ability of future generations to meet their own needs.”

Sustainable Diversion Limit

64. Minn. Stat. § 103G.287, subd. 2 states that groundwater appropriations may be authorized only if they avoid known negative impacts to surface waters. If the Commissioner determines that groundwater appropriations are having a negative impact to surface waters, the Commissioner may use a sustainable diversion limit or other relevant method, tools, or information to implement measures so that groundwater appropriations do not negatively impact the surface waters.

65. The DNR finds that authorized water use in the Little Rock Creek Area is having a negative impact on the Little Rock Creek stream ecosystem. As identified in paragraphs 44, 47 and 49, groundwater appropriations around Little Rock Creek are resulting in stream depletion of more than 20% of August median base flow. Paragraph 52 further identifies that stream diversion is causing ecosystem harm to Little Rock Creek.

66. Based on substantial evidence, limiting streamflow depletion to no more than 15% of the August median base flow protects the diversity of habitats represented in Little Rock Creek and therefore meets the statutory and rule criteria for protecting ecosystems and avoiding negative impacts to ecosystems.

67. Based on substantial evidence, DNR concludes that 15% of the August median base flow is the sustainable diversion limit for Little Rock Creek.

68. Based on the above analysis, the DNR has determined that 15% of August median base flow is 0.8 cubic feet per second at station H15029003, 1.1 cubic feet per second at station H15029001, and 2.9 cubic feet per second at station H1503100.

69. By establishing a sustainable diversion limit for groundwater appropriations, the DNR will consider groundwater-surface water interaction in determining how and when to limit water use based on limits that protect sufficient flow in Little Rock Creek, avoid negative impacts, and ensure compliance with Minn. Stat. § 103G.287.

Water Use Conflict

70. Minn. Stat. § 103G.261 establishes water use priorities in Minnesota. Minn. R.

6115.0740 defines a water use conflict. “For the purpose of these rules a conflict occurs where the available supply of waters of the state in a given area is limited to the extent that there are competing demands among existing and proposed users which exceed the reasonably available waters. Existing and proposed appropriations could in this situation endanger the supply of waters of the state so that the public health, safety, and welfare would be impaired.” This rule also defines the procedures by which the Commissioner will resolve the water use conflict. More specifically, the Commissioner shall evaluate the following:

• the reasonableness for use of water by the proposed and existing users;

• the water use practices by the proposed and existing users to determine if the proposed and existing users are or would be using water in the most efficient manner in order to reduce the amount of water required;

• the possible alternative sources of water supply available to determine if there are feasible and practical means to provide water to satisfy the reasonable needs of proposed and existing users.

Minn. R. 6115.0740, subp. 2(B).

71. Based on substantial evidence, including the modeling data described above in paragraphs 7, 9 21-23, 47 and 52 the DNR concludes that there is a water use conflict in the Little Rock Creek Area because competing demands exceed reasonably available waters. In particular, as described above, “total withdrawals” for agricultural irrigation in the Zone of Irrigation Influence at times exceed “established resource protection limits” – i.e., the sustainable diversion limit for Little Rock Creek – and therefore a conflict results among third priority water users. See Minn. R. 6115.0740, subp. 2 and ¶¶ 47 and 52.

72. As part of its analysis of the issues addressed in this Commissioner’s Order, DNR considered the…