Att_05_140P8421Q0104_NPS_Post-project_Hydrology_Report.pdf

Year Five of the Giacomini Wetland Restoration Project:

Analysis of Changes in Physical and Ecological Conditions in the Project Area

Lorraine Parsons and Amelia Ryan, Point Reyes National Seashore

With contributions from: Jules Evens, Avocet Research Associates;

Greg Kamman and Rachel Kamman, Kamman Hydrology and Engineering;

and Lindsey Sanders

October 1, 2015

Photo by Robert Campbell ii

Photo by Galen Leeds

Cite as:

Parsons, L., and A. Ryan. 2015. Year Five of the Giacomini Wetland Restoration Project: Analysis of Changes in Physical and Ecological Conditions in the Project Area. Point Reyes National Seashore, National Park Service.

4 Results and Discussion: Changes in Hydrology, Topography, and Sedimentation

Abiotic and biotic conditions within the Project Area are strongly swayed by – and tied to – changes in hydrology. One of the most dramatic changes in the Giacomini Wetlands after restoration was the sweeping expanse of water that spread almost immediately across the former dairy pastures with the twice-daily flooding of the tides. This change was predicted. However, what was less well understood was the process by which hydrology within the restored Ranch would evolve, similar to that of vegetation.

During planning for the restoration project, computer hydraulic modeling conducted as part of planning for the restoration project estimated that, based on existing and proposed elevations, 256 of the 550 acres in the East (area adjacent to Point Reyes Station) and West (area adjacent to Inverness Park) Pastures of the Giacomini Ranch would be inundated by tides daily or close to daily (KHE 2006). This modeling assumed that no levees would remain and that some tidal channels would be created. Larger tidal channels were built to jump-start marsh evolution, but only a few smaller tidal creek channels were constructed, with the assumption that most of the smaller channels would develop naturally over time. While levees were removed, the Undiked Marsh that had developed on the outboard of the levees was, in many cases, higher in elevation than the marshplains or former pastures. These marsh shelves, then, represent mini "levees" that can direct – or even constrain – flow within the former pastures.

Hydrologic changes were not notable after final removal of the West Pasture levees and completion of preliminary restoration activities in Olema Marsh in mid-October 2008 (KHE 2009a). However, very dramatic changes occurred almost immediately after final removal of the East Pasture levees on October 25, 2008 (KHE 2009a). Within days, much of the East Pasture -- and the very southern portion of the West Pasture -- was seemingly flooded.

During the first few months after breaching, Park Service staff monitored and mapped tide levels during higher high tide and low tide events to determine how well water levels in the Project Area corresponded with those predicted by hydraulic modeling. Additional monitoring was conducted in December 2009 of extreme high tides and low tides during neap tide conditions, with follow-up monitoring of low tides during spring tide conditions conducted in 2010, 2011, and 2012 and extreme high tides in 2011.

During 2008, 2009, and 2011, the upper extent of higher high tides appeared to match very well with that predicted by computer modeling, often mimicking the contour patterns exactly (Figure 4). In winter 2008, during tides ranging from 6.3 feet to 6.6 feet MLLW (5.8 feet to 6.1 feet NAVD88), tidewaters extended up to the 7.0 to 7.5 feet NAVD88 elevations in the East Pasture (NPS, unpub. data). Computer modeling predictions estimated maximum tidal elevations in the East Pasture of 7.15 feet NAVD88, with the area exposed to tidal influence at extreme tides being close to 282 acres (KHE 2006; Figure 3). However, while the maximum tidal elevations were sometimes greater than predicted, the amount of area in the East Pasture subject to extreme tidal influence turned out to be slightly lower than that predicted (251.7 acres), a difference of 11 percent (NPS, unpub. data; Figure 4). In 2009, the acreage of areas subject to high tides was only slightly less (242.5 acres), which probably resulted largely from the fact that mapping was conducted during an approximately 1 foot lower tide level (5.8 feet to 6.3 feet MLLW or 5.3 feet to 5.8 feet NAVD88; Figure 4). Otherwise, there appeared to be good agreement between 2008 and 2009 high tide extent. The maximum elevations reached by extreme high tides were a little more variable in the

Aerial oblique photograph of Giacomini Wetlands taken after levee breach. Northern portion of East Pasture or Shallow Shorebird area. Photograph: Courtesy of Robert Campbell Aerial Photography.

http://www.nps.gov/pore/parkmgmt/upload/planning_giacomini_wrp_restoration_water_fig02_08-09.pdf http://www.nps.gov/pore/parkmgmt/upload/planning_giacomini_wrp_restoration_water_fig01.pdf http://www.nps.gov/pore/parkmgmt/upload/planning_giacomini_wrp_restoration_water_fig02_08-09.pdf

West Pasture. During tides ranging from 6.3 feet to 6.6 feet MLLW (5.8 feet to 6.1 feet NAVD88), tidewaters extended up to the 5.75 feet to 7.0 feet NAVD88 elevations in the West Pasture (NPS, unpub.data; Figure 4). During extreme tides, tidal waters were predicted to reach a maximum elevation of

7.13 feet NAVD88 (KHE 2006; Figure 4). The variability in elevation extent in the West Pasture may result from the influences of freshwater, which may "push back" tidal influence where freshwater surface or groundwater flow is strongest.

Where computer modeling predictions diverged substantially from actual water levels was with low tide conditions. While mapped high tide water levels correspond pretty closely with predicted levels, water levels during lower low tides immediately after restoration were much higher than predicted by computer modeling. In other words, more area remained subtidal or permanently inundated than would have been predicted on elevation alone. Because channels were deliberately undersized to allow natural evolution, the width and density of channels were not large enough currently to fully accommodate flows, and waters were not fully draining on low tide, leaving a significant amount of water in East Pasture channels and marshplains even on the lowest low tides. Drainage problems were exacerbated by the fact that the outboard marsh shelves, which functioned as mini-levees, were funneling flows exclusively through the two primary tidal channel outlets that were created -- the Tomasini Slough, which flows into Lagunitas Creek near Railroad Point in the northern portion of the East Pasture, and, to a lesser extent, the new side channel for Lagunitas Creek, which drains the new Marshplain Enhancement area in the southwestern portion of the East Pasture.

Immediately after restoration, mapping of the permanently flooded areas during extreme low tide conditions indicated that water levels were not dropping below 4 ft NAVD88 in the East Pasture and approximately 3.75 ft -<4 ft NAVD88 in the West Pasture (NPS, unpub. data). Water level patterns in Lagunitas Creek were also affected: a flattening of the water level curve below 3.5 feet suggested that water levels in the creek were also dropping more slowly because of the added volume of water being conveyed by the marshplain (KHE 2009a). Prior to restoration, the morphology of gravel bars in Lagunitas and Fish Hatchery Creeks suggested that, after restoration, subtidal conditions would persist in portions of the Project Area below 2.0 ft NAVD88 in Lagunitas Creek and the East Pasture and 3.4 ft NAVD88 in the West Pasture due to the weir- or dam-type effect these gravel bars have on channel water levels (KHE 2006). In addition to changes on water level patterns, restoration also affected timing of tides, resulting in delays of low tides relative to predicted conditions at the nearby Inverness tide station by as much as 2 hours or more (NPS, unpub. data).

These dramatic hydrologic changes were most evident after restoration in the amount of subtidal area or areas that remained permanently inundated immediately after restoration. In the East Pasture, subtidal area under extreme low tide conditions (-1.7 ft to -0.4 ft MLLW or -1.2 ft to +0.1 ft NAVD88) totaled 109.4 acres immediately after restoration, compared to the 26.5 acres of subtidal area predicted under fully evolved conditions (NPS, unpub. data; KHE 2006; Figure 5). The discrepancy between restored and fully evolved conditions was not quite so great in the West Pasture, where subtidal extent predicted under fully evolved conditions (2.2 acres; KHE 2006) was only slightly lower than actual (7.4 acres; NPS, unpub.

data; Figure 5). Interestingly, subtidal extent was actually smaller under neap tide conditions – when the difference in elevation between low and high tides is substantially compressed – than under spring tide conditions, when low tides reach some of their lowest levels. In December 2009, subtidal areas totaled

52.9 acres in the East Pasture and 4.5 acres in the West Pasture when tides ranged between 1.9- to 2.7 feet MLLW (1.4- to 2.2 ft NAVD88). This represents almost a 51 % reduction in subtidal area with only a 1- to at most 3- foot difference in tidal water elevation. These results suggested that drainage was being constrained by the larger volume of water that flowed into the newly restored wetland on a spring tide, when high tides are very high, than on a neap tide, when high tides are lower.

Circulation and drainage patterns are expected to be further altered in the future by changes in Lagunitas Creek and interior tidal channel geometry. Immediate post-project surveys in 2009 had indicated a uniform increase (1.0 ft) in bed elevation of the mainstem Lagunitas Creek channel mid-way through the Project Area relative to elevations in 2003 (KHE 2009b). In contrast, channel elevations at the downstream end of the Project Area (near the former North Levee area) remained fairly comparable in 2009 to those measured in 2003 by the USGS (KHE 2009b).

http://www.nps.gov/pore/parkmgmt/upload/planning_giacomini_wrp_restoration_water_fig01.pdf

Since restoration, elevations within the Lagunitas Creek cross-sections have not changed appreciably, with the exceptions of shoals at channel outlets (KHE 2011a, KHE 2012a). In 2009, ebb shoals or gravel bars developed at the mouth or downstream of the mouth of the newly constructed channels draining the East Pasture, with accretion during the first year totaling more than 1 to 2 feet (KHE 2009b). These deltaic-type shoals had encroached into the mainstem Lagunitas Creek channel, reducing the cross-sectional flow area, although they did not span the full width of the channel (KHE 2009b). While both of these shoals rapidly formed after restoration, their evolutionary paths have diverged somewhat. The horseshoe-shaped Tomasini Slough outlet shoal remained relatively consistent in elevation between 2010 and 2011. It is comprised of an inner and outer shoal that range in elevation from 1- to 2 feet NAVD88 (KHE 2011a), although, based on water level results, it may have increased in elevation in 2012 (KHE 2012b). Conversely, the shoal at the mouth of the new side channel off Lagunitas Creek has continued to accrete or build in elevation with estimated deposition rates of 0.7 feet in WY 2010 and 0.75 feet in WY 2011 (KHE 2011a). Shoal build-up slowed in 2012, with elevations increasing only by a few inches (KHE 2012a). With post-restoration winters being relatively dry, little energy in the way of flood scour has been available to counteract deposition of sediments at the mouth of new tributaries to Lagunitas Creek, which has led to a net depositional environment. Should flood flows continue to be reduced, shoals will continue to build in Lagunitas Creek and perhaps change circulation and drainage patterns in the creek and wetland.

While elevations may have increased at the mouth, both of the newly constructed channels have actually deepened since restoration was completed. By 2010, the downstream portions of Tomasini Slough had decreased in elevation relative to constructed elevations by as much as 1.8 feet, with an additional drop of 0.75 feet during 2011 (KHE 2011a). Between 2011 and 2012, channel bottom elevations in Tomasini Slough remained relatively stable (KHE 2012a). The one upstream station on Tomasini Slough for which pre-restoration elevation data exist showed little elevation chance since pre-restoration conditions (KHE 2011a). A similar pattern of channel incision occurred at the newly created side channel off Lagunitas Creek in the East Pasture. At least 1 foot of both channel deepening and widening took place in downstream portions of this small tidal creek, while upstream portions widened, but actually became more shallow through deposition of approximately 1 foot of sediment (KHE 2011a). Channel incision rates slowed in 2012 (KHE 2012a). Unconstructed channels are also becoming deeper: these are naturally developing channels on the marsh floodplain.

Unfortunately, the lack of vegetation, particularly in the northern portion of the East Pasture, may slow down this process somewhat by encouraging overflow of tidal waters and floodwaters onto the marshplain rather than keeping them in channels (KHE 2010a). Indeed, in WY 2012 or Year 4, there was minimal to no change in tidal creek channel morphology, with only some channel widening at two of the cross-sections (KHE 2012a). With little flood flow available for landscape reworking, the tides must do the work, and tidal energy within the restored wetlands is dampened by the shoals off Tomasini Slough and the Lagunitas Creek side channel (KHE 2012a). As downstream reaches deepen in future years, steepening channel gradients will propagate upstream, and channels will scour, if needed (KHE 2012a).

Interestingly, marshplain areas increased in elevation in both the East and West Pastures, despite the lack of sediment input from flood flows and the massive vegetation die-off in the East Pasture that would have been expected to compact soils due to loss of root volume below the soil surface ( Appendix A;

Parsons and Ryan 2014). In both pastures, elevation gains between 2008 and 2010 exceeded sediment deposition rates measured through use of feldspar markers, with elevation gains ranging during that period from 12.7 mm in the West Pasture to 19.2 mm in the East Pasture and sediment deposition rates for that same period ranging between 0.9 and 5 mm annually in the East and West Pastures (Appendix A). In 2011, the trends in elevation shifted somewhat, with elevation again increasing in the West Pasture (4.5 mm) relative to 2010 elevations, but decreasing in the East Pasture (-3.6 mm), although, overall, elevations were still considerably higher in the East Pasture post-restoration than pre-restoration (Appendix A). In 2012 and 2013, elevations in the East Pasture increased again, with annual elevation gains ranging from 8.0 to 10.1 mm (Appendix A). Interestingly, some of the other sampling sites that had not appeared to gain in elevation since 2008 such as the ones at Walker Creek Marsh in the northern end of Tomales Bay had positive elevation increases for the first time in 2011 (4.5 mm), and this trend continued in both 2012 and 2013 (Appendix A). Considering that elevation gains typically exceed sediment deposition rates, most of the elevation gains in the restored wetlands appear to result from changes in subsurface processes, with reintroduction of tides potentially increasing porewater volume in the soils and slowing down subsurface oxidation rates of organic matter (Appendix A).

As discussed earlier, most of the sediment deposition occurring in Lagunitas Creek and the Project Area appears to come from re-working of soils from the Project Area, which are now exposed and vulnerable after construction grading and decay of pasture vegetation. With the first winter being a dry one, sediment inputs from the upper watershed were probably minimal, particularly as there were no overbank flooding events. While the Year 2 winter was much wetter, there was still not enough flow volume during storm events to cause overtopping of creek banks in the Project Area, and, thereby, any deposition of sediment on newly restored marshplains. Some overtopping did occur during the winter of Year 3, when rainfall totals were even higher than Year 2, but there was only one very brief event. Even during large storms, most of the peak flood flow and sediment generated are trapped by upstream dams, reducing flood volume and sediment loading to downstream areas. The winters of Years 4 and 5 have generally been drier than normal, so flood flows have also been lower than normal, with the exception of December 2012, when almost 12 inches of rain fell, but most of the surface run-off generated by this series of storms was captured behind the dams.

Despite this lack of overbank flooding, sedimentation monitoring has shown that sediment was still deposited on Project Area marshplains during the last five years (Appendix A). Dry winters and reduced flood flow volume have led to a net depositional environment both within the Project Area and other marshes, except where flow velocity is high enough to counteract this trend, such as in the downstream portions of the Tomasini Slough and the Lagunitas Creek side channel. With overbanking flooding during storms being minimal, much of this sedimentation may derive from re-working of Project Area soils (KHE 2012a). Any existing tidal energy in these systems is being used primarily to transport sediment rather than scour channel banks and beds (KHE 2012a).

Annual deposition rates since restoration in the northern portion of the East and West Pastures appeared higher than in other sites in Tomales Bay and lower than in Limantour Estero, however, differences were not statistically significant (GLM, df=3, F=2.12, P=0.11; Appendix A). Average annual sedimentation rates since restoration in the Giacomini Wetlands have ranged from 0.9 to 8.1 mm/year, compared to 0.7 to 3.0 mm/year in other Tomales Bay sites (Appendix A). Since restoration was implemented, the lower-elevation, more-deeply-subsided East Pasture area appeared to have a higher average annual sedimentation rate (6.1 mm/year) than the higher-elevation West Pasture area (1.9 mm/year; Appendix A). The Limantour sites had a higher range of annual sediment deposition rates than Tomales Bay ones, with average rates ranging from 1.6 to 4.2 mm/year (Appendix A). These numbers are still seemingly lower than historic sediment deposition rates in Tomales Bay, which were estimated to average 5 mm/year (Rooney and Smith 1999). In San Francisco Bay, current short-term accretion rates appear to range between 3.1 and 5.9 mm/year, with higher rates at lower-elevation marshes (Callaway et al. 2012).

Essentially, the Giacomini Wetlands are in the process of hydrologic evolution. The conditions predicted by hydraulic modeling represent a later phase in wetland development.

Over the coming years, existing and created channels will continue to increase in size to accommodate flood flows, and new tidal channels will develop, increasing exchange between the restored wetland and Lagunitas Creek and creating closer to equilibrium between tidal inflow and outflow. In addition, some portions of the higher elevation Undiked Marsh outboard of the levees may continue to erode (as they have been doing prior to restoration), allowing more tidal waters to sheetflow across the marshplain back into Lagunitas Creek. Some of these changes may be accelerated during flood events, although storms so far have not been of sufficient magnitude to dramatically alter the Developing tidal channel wetland landscape.

This evolution appears to be already well underway. Hydrologic data suggested that the marsh was draining slightly faster during outgoing or ebb flows in 2009 than 2008 (KHE 2010a), and drainage improved slightly again between 2009 and 2011, at least during spring tides (KHE 2011b). Low tide elevations continue to be constrained as they were prior to restoration by the presence of gravel and sand bars at the mouths of creeks, which keep water levels at about 2.0 feet NAVD88, although, in 2011, water levels repeatedly dropped below 2.0 feet NAVD88 (KHE 2011b). In 2012, however, maximum low tide elevations increased slightly within the East Pasture, possibly due to a build-up of the Tomasini Slough shoal, with water levels almost never dropping below 2.0 feet NAVD88 (KHE 2012b).

This improvement in drainage efficiency can be seen in the dramatic declines over the last few years in the extent of subtidal areas during an extreme low tide. Acreage declined from 109.4 acres in the East Pasture immediately after restoration to 68.1 acres in summer 2010 under approximately equivalent tide conditions (-0.44 to -1.74 ft MLLW in 2008 vs. -1.54 to -1.67 ft MLLW in 2010, Figure 5). This represents a 38% decrease in extent of permanent inundation during extreme low tides within two years. In 2011, this trend appeared to continue (Figure 3): acreage of subtidal areas in the East Pasture dropped to 51.0 acres, even though water levels may have been influenced somewhat by the unusual rainfall pattern in WY 2011, where precipitation extended well into the summer. (Summer stream discharge flows averaged 10 cfs compared to the median estimate of 6 cfs, which may have kept the marsh from fully draining during low tide events.) This situation demonstrates that ecosystem evolution following restoration is not a linear process, but can occur in distinct stages or phases that involve triggering or exceeding thresholds before the wetland moves into the next evolutionary stage or phase.

References:

Kamman Hydrology & Engineering (KHE; 2006). Hydrologic Feasibility Assessment Report: Giacomini Wetland Restoration Project. Point Reyes National Seashore. Point Reyes Station, California, Prepared for Point Reyes National Seashore.

KHE (2009a). Olema Marsh Restoration: Salinity Impact Assessment. Prepared for Point Reyes National Seashore, Point Reyes Station, California.

KHE (2009b). Evaluation of recent topographic profiles at selected locations in Lagunitas Creek

KHE. 2010. Giacomini Wetlands 2009 Monitoring Data Summary. Prepared for Point Reyes National Seashore Association.

KHE (2011a). Giacomini Wetlands 2009 Monitoring Data Summary. Prepared for Point Reyes National Seashore, Point Reyes Station, California.

KHE (2011b). Survey of Cross-Sectional Profiles in the Giacomini Wetland Restoration Project Area.

Prepared for Point Reyes National Seashore, Point Reyes Station, California.

KHE (2012a). Giacomini Wetlands 2009 Monitoring Data Summary. Prepared for Point Reyes National Seashore, Point Reyes Station, California.

KHE (2012b). Survey of Cross-Sectional Profiles in the Giacomini Wetland Restoration Project Area.

Prepared for Point Reyes National Seashore, Point Reyes Station, California.

Parsons, L and A Ryan (2014). Keeping Pace with the Tides: Results of SET and Marker Horizon Monitoring – Giacomini Wetland Restoration Project, Tomales Bay. Point Reyes National Seashore.

Rooney, J.J. and S.V. Smith (1999). Watershed landuse and bay sedimentation. Journal of Coastal Research, 15(2): 478–485

Figure 3. Predicted Tides

Figure 4. High Tides

Figure 5. Low Tides Low tidelines under spring and neap tide conditions since restoration was implemented. Colored areas represent inundated areas under extreme low tide conditions. Predicted refers to areas that were predicted by hydrologic modeling to remain subtidal or inundated under fully evolved marsh conditions.

5 Results and Discussion: Changes in Water Quality

One of the primary objectives of the Giacomini Wetland Restoration Project was to improve not only the quality of water within the former dairy ranch itself, but the quality of water flowing downstream to Tomales Bay. For more than 60 years, the levees constructed by the Giacominis essentially funneled all flows from the upper part of the Lagunitas Creek watershed directly to Tomales Bay. Three major creeks actually merge just upstream of the Giacomini Wetlands: Lagunitas Creek, Olema Creek, and Bear Valley Creek, which flows through Olema Marsh. These creeks represent a sizeable amount of the freshwater inflow—and potential pollutant load—to Tomales Bay, with more than 66% or two-thirds of Tomales Bay’s freshwater input coming from this drainage (Fischer et al. 1996). Additional inflow to Lagunitas Creek comes from Tomasini Creek, which flows through the East Pasture adjacent to Point Reyes Station, and Fish Hatchery Creek, which flows through the West Pasture adjacent to Inverness Park. These creeks also represent potential sources of pollutant loading from non-point surface run-off, leakage from septic systems, agricultural drainage, and, in the case of Tomasini Creek, potentially leaching from an improperly closed landfill.

Water Quality Conditions within the Wetlands Prior to Restoration

Of course, not all the pollutants came from upstream portions of the watershed. The dairy also represented a sizeable source of potential pollutants to Tomales Bay. During full-scale agricultural operation, the East Pasture was intensively managed through construction and frequent dredging of ditches, manuring of pastures, and grazing of several active dairy herds. The West Pasture, which was located across Lagunitas Creek from the dairy facility, was less intensively managed and grazed.

Practices such as frequent dredging of ditches led to some of the pasture ditch waters, particularly in the East Pasture, being very low in oxygen -- low enough to impact and perhaps even kill aquatic organisms (Parsons 2009).

Not surprisingly, concentrations of nutrients and pathogens were typically highest in the dairy relative to levels in Lagunitas Creek, other creeks flowing into the Giacomini Ranch, or natural tidal marshes in Tomales Bay (Parsons 2009). One of the predominant nutrients in Tomales Bay is nitrates. The relatively well oxygenated conditions present in most of the Study Areas -- except the East Pasture ditches -- may have contributed to the dominance of nitrates as the primary source of nutrients (Parsons 2009). For pollutants such as nitrates, pulses appeared to substantially drive nutrient dynamics more than consistent loading, as median concentrations (central values) of nitrates within the dairy (0.83 mg/L) were not much different from those in natural marshes (0.7 mg/L; ibid).

However, mean nitrate concentrations, which reflect the influence of "spikes" or "pulses," showed greater disparity, with concentrations averaging 7.25 mg/L (NO3-) for the East Pasture and dropping below 1.1 mg/L for other areas (Parsons 2009). Another form of nitrogen, ammonia, typically present in more low-oxygen environments, was only infrequently detected during pre-restoration sampling, but of the 64 detections of ammonia during the study, more than 47% of them occurred in the East Pasture (Parsons 2009).

In general, pathogens represent one of the major water quality issues facing Tomales Bay. While seemingly pristine, the Bay and its surrounding watershed generate a considerable volume of pathogen indicator bacteria, total and fecal coliform, because of the large amount of land in agricultural use, leaking septic systems in the many rural residential communities perched on the Bay’s edge, and other factors such as bilge discharge from boats. With Giacomini Ranch supporting a considerable number of dairy cattle during its operation, pathogen concentrations were definitely elevated relative to natural waters.

Cows at Giacomini Ranch prior to restoration

Prior to restoration, the Project Area had substantially higher estimated median concentrations of fecal coliform (1,600.9 mpn/100ml) than natural marshes (72.0 mpn/100 ml), although, based on results of statistical analyses, seeming differences with upstream areas or source creeks (705.6 mpn/100 ml) might have been obscured by high variability in the data (Parsons 2009). Not surprisingly, the heavily managed East Pasture had significantly higher estimated levels (6,298.8 mpn/100 ml) than most of the other areas sampled, with the possible exception, from a statistical standpoint, of Olema Marsh (1,821.4 mpn/100 ml;

ibid). Estimated geometric means or medians for all other areas ranged between 356.9 mpn/100 ml for downstream Lagunitas Creek to 1,131.7 mpn/100 ml for the West Pasture (ibid).

While concentrations of nutrients and pathogens were highest in the dairy, loading or the volume of pollutant was actually highest in the creeks or upstream areas flowing into the restoration Project Area and, eventually, into Tomales Bay (Parsons 2009). These results are not surprising. The East Pasture was entirely leveed and was only hydrologically connected to Lagunitas Creek during periods when the pump was actively operated or when floodwaters overtopped the levees and flowed through the pasture to drain out via the spillways at the ranch’s northern end. The West Pasture functioned as a muted tidal system in that a somewhat leaky one-way tidegate on Fish Hatchery Creek’s downstream regulated inflow and outflow into the pasture. There were some exceptions. For example, for fecal coliform, estimated loading rates for the restoration Project Area (mean=249,389 mpn/s) were lower than upstream area or source creeks (mean=3.86 million mpn/s), but higher than natural marshes (mean= 60,094.1 mpn/s; ibid). Conversely, natural marshes had the highest loading rates for phosphates (0.15 mg/s), with rates for the restoration Project Area (0.03 mg/s) and upstream areas or source creeks (0.06 mg/s) much lower, which may relate to the more substantial marine influence on natural marshes (ibid).

As with many other parameters, loading rates or pollutant volumes were typically driven by pulses or spikes, particularly during storm events. The importance of storm events to downstream loading is evident in the disparity between mean (10.11 mg/s) and median (0.66 mg/s) instantaneous loading rates for nitrates on Lagunitas Creek: during an April 2006 storm, rates reached as high as an estimated 220 mg/s (Parsons 2009). Research on other agricultural watersheds has also documented the highest export of nutrients and pathogens in stormflow, with levels generally higher in the wet season than the dry season (Vanni et al. 2001, Lewis and Atwill 2007).

Ironically, storms were the least sampled due to inherent planning and logistical difficulties, however, we increased efforts in later years to capture storm events in the monitoring record.

Water Quality Conditions After Restoration

Restoration of the Giacomini Wetlands has actually occurred in several distinct phases. While the Giacomini family had a Reservation of Use Agreement that allowed them to operate through fall 2007, the family elected to sell off their main dairy herds in 2006 and instead a graze a smaller number of dairy heifers or young cows. From that point in 2006 through construction in fall 2008, the restoration process began to occur, but in a more passive manner. Most of the active agricultural management -- including ditching and manure-spreading -- was discontinued in 2006 with limited irrigation and grazing continued until fall 2007. Phase I of construction in fall 2007 involved removal of most of the agricultural infrastructure -- barns, pipelines, fencing, and surface scraping of the manure slurry disposal pasture -- as well as removal of the southernmost levee in the East Pasture. However, full restoration, which hydrologically reconnected the former historic marsh to Lagunitas and Tomasini Creeks, was not realized until October 2008, when the levees on both the East and West Pastures were fully removed.

Pipe conveying waters from former Giacomini Ranch

Analyses performed as part of environmental compliance predicted that water quality conditions within the restored wetlands would remain similar or even worsen immediately after restoration before showing improvement over the long-term (NPS 2007). While removal of cows, manure, and agricultural practices such as ditching would be expected to improve water quality, improvement was not expected to happen overnight due to high levels of nutrients and pathogens in present. In addition, conversion of the pasture back to marshland would cause a massive die-off in mostly non-native pasture grasses and herbs that would, upon breakdown by bacteria, release large amounts of organic and inorganic nutrients into overlying waters. Changes in water salinity and hydrologic regime would also affect soils, most of which have high nutrient -- and possibly pathogen -- levels from decades of agricultural management. Nutrients would be expected to flux or move out of the soils into overlying waters, as well, in response to changes in soil chemistry. With accelerated breakdown of organic matter both above and below-ground would come higher demands on oxygen in water and soils, leading to possible episodes of oxygen depletion in overlying waters. Breakdown of organic matter could also lead to decreases in pH from release of humic acids. The die-off of vegetation and resulting increase in bare ground would also be expected to exacerbate turbidity issues resulting from disturbance of soils during construction for creation of new tidal channels and excavation of certain areas to lower intertidal elevations.

Interestingly, during the first water year after restoration (October 2008 through September 2009), most of the anticipated short-term negative impacts to water quality within the restored wetlands were not observed (Parsons 2010). Rather, there was a general improvement in overall water quality conditions that occurred at a much more rapid pace than initially anticipated (ibid). Remarkably, despite the fact that movement of sediment from the wetland was evident in shoaling at creek mouths in Lagunitas Creek (KHE 2009), turbidity levels with wetland waters remained equivalent to pre- and passive restoration conditions during Year 1 or the first year after restoration (Parsons 2010). Lower turbidity levels may have been driven to some degree by the dry conditions during the 2008–2009 winter, but sampling events did capture at least two small to moderately sized storm events (ibid).

The influence of storm events was perhaps more evident in Year 2 (October 2009 through September 2010). While there were no statistically significant differences in turbidity levels between pre-and post-restoration in Year 1, differences did exist between pre and post-restoration in Year 2, with mean turbidity levels more than tripling from 15.7 NTU to 60.8 NTU during Year 2 (Parsons 2011). In WY 2009/2010, rainfall totals jumped, and 50% of the sampling events occurred moderate to large storm events, although there was still no overbank flooding, at least from Lagunitas Creek. The fact that turbidity levels were significantly higher in the Project Area than in the Reference Areas suggests that turbidity levels in the restoring wetlands exceeded those that would be expected in mature marshes simply based on normal sediment resuspension pulses during storm events. Therefore, Year 2 may better represent the short-term increase in turbidity levels immediately after restoration that was predicted in the environmental compliance analysis documents.

Turbidity during subsequent years dropped relative to Year 2, but still remained higher in Year 3 (21.3 NTU), Year 4 (32.6 NTU), and Year 5 (28.2 NTU) than in Year 1. Overall, turbidity has increased by 44% after the levees were breached, however, differences in the Project Area between treatment periods was only weakly significant (GLM, df=2, F=2.37, P=0.09; log-transformed). A statistically significant interaction existed between year and Study Area (GLM, df=4, F=4.98, P=0.001; log-transformed), suggesting that turbidity differences do exist between the restored marsh and natural marshes, but that this difference is mediated is somewhat by temporal differences. Turbidity levels in natural marshes actually dropped following restoration approximately 20%.

Following levee breaching, mean oxygen levels in the Project Area increased 16% from 7.30 during Pre- Restoration to 8.55 mg/L during Passive Restoration and to 8.50 mg/L during Full Restoration (GLM, df=2, F=31.2, P<0.001; log-transformed). Lower D.O. levels occurred in Year 2 than Years 1, 3, 4, and 5:

both Years 2 and 3 were quite wet, although the Year 2 sampling approach may have captured more storm events. Cold temperatures and strong flow conditions could suppress biological activity in waters relative to warmer, more quiescent periods. Improvement was especially marked in the East Pasture, where mean oxygen levels climbed 72% from 4.98 mg/L pre-restoration to 8.58 mg/L after restoration.

With restoration, oxygen concentrations might have been expected to decrease -- or only increase slightly overall – due to the abundant organic matter that die-off of pasture vegetation that has been released into Project Area waters during the first year and even second year of restoration. With high levels of organic matter, bacteria become extremely active and rapidly deplete oxygen levels in overlying waters, particularly during the night, when oxygen stores are not replenished through primary production. While pasture vegetation went through multiple stages of die-off in the first year with some die-off in the second year, the effect of this die-off was not evident in Project Area oxygen concentrations, and, in fact, by the fifth year following restoration, oxygen levels in the Project Area were equivalent to those in Reference Areas or natural marshes (GLM, df=1, F=0.01, P=0.91; log-transformed).

The temperature of waters in the restored wetlands depends to some degree on the temperature of the waters flowing into it, as well as what happens to that water once within the wetland. Temperatures might have been expected to increase perhaps with reintroduction of warmer tidal waters to the former freshwater-dominated dairy, although an increase in daily exchange of waters with adjacent once levees were removed could also act to lower water temperatures. Since breaching of the levees, mean temperatures dropped by 4% within the Project Area from 15.9 degrees Centigrade Pre-Restoration to

14.2 degrees Centigrade during Passive Restoration and to 15.3 degrees Centigrade during Full Restoration (GLM, df=2, F=7.40, P=0.001; log-transformed). This temperature decline could have simply reflected the change in hydrologic regime within the restored wetland. However, an even larger decline (10%) occurred in natural marshes following 2008 -- even in those that are too distant to have been affected by restoration. This suggests that more regional or watershed-scale factors affected temperature regimes such as climatic patterns, which is supported by the fact that temperature varied significantly between years following restoration among the Study Areas (GLM, df=4, F=4.84, P=0.001; log-transformed). Years 2 and 3 had higher-than-average rainfall, and stormwater-influenced creek flows are colder than tidal waters. These regional factors may have narrowed any differences that might have otherwise existed between the newly restored wetland and natural marshes, as temperature did not differ between Study Areas during the post-restoration period (GLM, df=1, F=0.03, P=0.87; log-transformed).

Similarly, the alkalinity or pH of waters also reflects both the pH of source waters, as well as conditions within the wetland. Most creeks feeding into the Project Area actually have fairly high or basic pHs (range = 7.7–8.1) regardless of differences in geologic substrate between the granitic Inverness Ridge and the Point Reyes Mesa coastal marine terrace and surrounding Franciscan Formation hills, which are separated by the San Andreas Fault that created this tectonic estuary (Parsons 2009). This pH range is similar to that of tidal waters. Lower pH waters (~5.9–6.6) only occur in areas where there is more extensive influence from groundwater (ibid). Groundwater substantially influenced the hydrology of the former ranch, because the levees impounded this subsurface flow.

While introduction of full tidal flows to the Project Area might have been expected to boost pH, the median pH in the Project Area has actually decreased as much as 4.6% since dairy operation from 7.60 during Pre-Restoration to 7.30 during Passive Restoration and to 7.25 during Full Restoration (Figure 6). A significant interaction existed between Study Area and treatment period, with pHs dropping most in Upstream Areas (6.6%) since pre-restoration (GLM, df=4, F=4.35, P=0.002). Median pH in the Project Area during the first five years after restoration was 7.25 during Year 1, 7.14 during Year 2, 7.26 during Year 3, 7.21 during Year 4, and 7.37 during Year 5 (Figure 6).

The seeming drop in pH could be attributed a number of factors. First, the increase in hydrologic exchange and decrease in water residence time may have reduced the influence of phytoplankton blooms on pH relative to pre-restoration conditions: phytoplankton or algal blooms tend to drive up the alkalinity of waters (Parsons 2010). Secondly, breakdown of organic matter from extensive die-off of pasture vegetation can also increase release of humic acids into overlying Project Area waters, resulting in a decrease in pH. In addition, other biogeochemical processes can cause release of acidic substances into overlying waters when soils of tidal wetlands are dry for long periods of time. For example, flushing of sulfuric and iron-associated acids from oxidation of reduced sulfur and iron in soils into overlying waters can also decrease pH: sulfuric and iron-associated acids are generated when pyrites or other reduced or anoxic forms of sulfate and iron in the soil are oxidized and broken down or converted during drawdown or low-water periods, with soluble acids from oxidation then released into overlying waters when tidal exchange is reintroduced. The Project Area was deliberately dried out before and during construction to improve constructability conditions, resulting in even drier conditions than when the Project Area was ranched.

Most of these factors relate to possible changes in physical and biological conditions that may have occurred as a result of restoration. However, a similar slight, but significant, decrease in mean pH was also observed in natural marshes, including in areas that were not necessarily affected by the restoration (Figure 6). In Reference Areas, pH dropped from a mean of 7.67 and 7.53, respectively, during Pre- Restoration and Passive Restoration sampling periods to 7.34 during Full Restoration (Figure 6). In evaluating the data more closely, it appears that the median pH for Reference Areas started declining in WY 2007 prior to restoration and continued declining each year until WY 2010, when median values at least appear to have roughly stabilized around 7.30 – 7.35 (Parsons 2012). The largest declines were observed at the Undiked Marsh directly north of the Giacomini Wetlands and Limantour Marsh in Limantour Estero (ibid).

The changes in these two natural marsh systems could relate directly to the fact that, in both cases, upstream areas have been restored, and restoration could be affecting the pH of downstream marshes, as well as that of the Project Areas. However, pHs in more distant areas of Tomales Bay appear to have also been lower during this period, as well. University of California, Davis, (UC Davis) researcher Ann Russell and her colleagues temporarily reoccupied the Tomales Bay sampling stations established by the Land Margin Ecological Research (LMER) program in the 1980s as part of a current research effort to understand the impacts of ocean acidification and climate change on estuarine invertebrates. During LMER, sampling was conducted at 10 stations from the outer Tomales Bay near the mouth to the southernmost one some distance north of the Undiked Marsh between 1987 and 1995. Russell reinitiated sampling in fall 2008 just when the restoration project was almost complete. During sampling efforts from 2008 to 2010, Russell has found no difference in most of the field parameters between the historic LMER data and recently collected data, however, pH did appear to have declined in both the outer and inner Bay by as much as 0.25 pH units (A. Russell, UC Davis, pers. comm.).

While apparent decreases in pH in Tomales Bay and its marshes might lead to questions about the effect of ocean acidification on pH of tidal waters flowing into estuaries, there are several factors that argue against the findings of our monitoring and Russell’s being connected to ocean acidification. While Russell and colleagues did observe larger decreases in pH in the Outer Bay relative to the Inner Bay (Russell et

al. 2010), in our results, pH decline appears to have been greatest furthest from the mouth of the estuary.

Russell also believes that the change observed in pH for Tomales Bay was too large to be attributable to dissolution of CO from the atmosphere into estuarine waters (A. Russell, UC Davis, pers. comm.).

However, not all carbon inputs into the estuary come from the atmosphere (ibid). In addition to changes in pH, concentrations of dissolved organic carbon (DOC) and, in the Outer Bay, dissolved inorganic carbon (DIC) also appeared higher relative to the LMER program sampling period (Russell et al. 2010).

Some of these differences may relate to the fact that the sampling period during the study implemented by Russell and her colleagues was wetter than the LMER sampling one (J. Largier, UC Davis, pers.

comm.). This would also affect transport of carbon from the upper watershed into the Bay. At least in terms of the Park Service’s dataset, cumulative rainfall volume did appear equal to or very slightly higher during the post-restoration sampling period (mean for Oct 2008-Sept 2013 =1.00 in > normal) than the pre-restoration one (mean for Oct 2004-Sept 2008=0.70 in>normal). Higher rainfall would increase freshwater inflow from both surface water and groundwater sources, which can have lower pH values than tidal waters in our Study Area: this is evident in the generally lower range of values for the Upstream Areas during the post-restoration sampling period (Figure 6). In particular, groundwater outflow in this area tends to have a slightly lower pH: these factors could affect pH within the restored wetlands, above and beyond any restoration effect. In addition, while these pH changes may be unrelated to ocean acidification, it does not rule out that we may begin to see changes related to climate change in future years, although pH in estuaries is normally more highly variable than that of oceans even without the influence of climate change.

As noted earlier, nitrates are one of the predominant nitrogen sources in the Tomales Bay watershed, and levels were elevated in the former dairy ranch prior to restoration. Immediately following breaching of the levees, nitrates did actually show a sharp pulse, with levels in newly restored waters averaging 3.44 mg/L (Parsons 2010; Figure 7). However, concentrations dropped dramatically in subsequent sampling events, which included two storm events (Figure 7). By January 2009, estimated concentrations had dropped to an average of 0.18 mg/L and median of 0.13 mg/L, with May 2009 (average=0.02 mg/L) and August 2009 (average=0.06 mg/L) even lower (ibid).

Since restoration, mean nitrate concentrations (1.02 mg/L) have fallen at least 68% relative to those recorded prior to restoration (3.22 mg/L; P<0.0001) and during Passive Restoration (4.52 mg/L; P=0.06;

GLM, df=2, F=16.5, P<0.0001; Figure 7). Similar to average values, estimated median nitrate values dropped 70% from 0.83 mg/L Pre-Restoration to 0.37 mg/L during Passive Restoration and to 0.25 mg/L during Full Restoration (Mood Median, df=2, Chi-Square=49.8, P<0.0001).

The strong disparity between mean and median levels for nitrates in the Project Area suggest that certain sites or sampling events are substantially influencing results by elevating mean nitrate levels. One factor affecting results is a non-point source discharge from Point Reyes Station into one of the restored wetland features, which sporadically causes large spikes in nitrate concentrations. This “upstream” sampling location exceeded the U.S. Environmental Protection Agency maximum standard of 10 mg/L during every sampling event in Years 2, 3, 4, and 5 and 75% of the events in Year 1 (Figure 7). Not surprisingly, the highest nitrate levels in the restored wetland during Years 3, 4, and 5 occurred in the Tomasini Triangle Pond, which is a created freshwater marsh acting as the receiving water for this non-point source discharge. The pond may also be affected by septic- influenced groundwater from the Point Reyes Mesa.

In addition to non-point source run-off, nitrates do appear influenced – if not completely driven – by watershed-scale factors such as weather patterns. The possible influence of larger scale factors such as precipitation patterns may account for the observed drop in nitrate levels in natural marshes, as well as the restored one, after 2008. Estimated mean nitrate levels in natural marshes decreased after the Pre- Restoration period from 0.88 mg/L to 0.36 mg/L during Passive Restoration (~2007 – 2008) and then climbed slightly again to 0.50 mg/L during the full restoration sampling period (Oct 2008 to Sept 2013;

GLM, df=2, F=29.3,…