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While nitrate concentrations and loads showed improvements in Walnut Creek watershed, herbicides, fecal coliform and phosphorus did not show consistent evidence for water quality changes. It is suspected that the main reason for this difference can be traced to the manner in which NPS pollutants are delivered to streams. Unlike nitrate that is primarily discharged to streams with groundwater seepage and tile drainage, herbicides, fecal coliform and phosphorus are primarily delivered via surface runoff. Whereas nitrate concentration patterns vary according to a near normal distribution in a year, annual concentration patterns of runoff driven pollutants are highly skewed and often vary several orders of magnitude between stormflow and baseflow. Because of this variability, sampling strategy becomes critical for detecting water quality changes in surface water. Water sampling on a fixed interval basis, as used during this project, did not routinely monitor storm

Year A d ju st ed IBI Sc ore 0 10 20 30 40 50 Walnut Squaw 19 95 19 96 19 97 19 98 19 99 20 00 20 01 20 02 20 03 20 04 20 05

Figure 70. Summary of annual Walnut and Squaw creek IBI scores.

events when the majority of runoff-pollutants are delivered to streams. Since baseflow constitutes a majority of total streamflow, a fixed sampling interval will be biased toward collecting baseflow water samples. During the few sampling days that corresponded to runoff events, high concentrations of herbicides and phosphorus were detected. Several high flow events sampled during this study occurred during the last years of the project that, in all likelihood, skewed the time-series trend analyses and load estimation.

This was particularly reflected in atrazine concentration patterns. Despite atrazine restrictions on refuge-owned lands that reduced atrazine applications by an estimated 28 percent, atrazine continued to be detected in Walnut Creek and subbasins at frequencies and concentrations no different than Squaw Creek.

And yet, a baseflow synoptic sampling completed in 1999 revealed large differences in atrazine losses within Walnut Creek refuge that were not observable by the fixed interval monitoring. It seems unlikely that the large reduction in atrazine applications that occurred in Walnut Creek watershed, compared to a probably increase in applications in Squaw Creek associated with increased row crop, would not have resulted in a statistically significant decrease in herbicide concentrations in Walnut Creek. Thus, changes in surface water concentrations of atrazine and other herbicides may have occurred but they could have been missed by the sampling design.

The lack of significant changes in fecal coliform concentrations at the watershed outlets WNT2 and SQW2 may point to poor sampling design or to an insufficient amount of change

Reference Sites REMAP Sites

Metric

Mean

Score 95% CI

Mean

Score 95% CI Native Fish Species Richness 6.5 5.9 - 7.1 5.7 4.8 - 6.7 Number of Sucker Species 4.4 3.5 - 5.4 2.6 0.9 - 4.3 Number of Sensitive Species 1.4 1.0 - 1.9 1.0 0.3 - 1.7 Number of Benthic Invertivore Species 4.6 3.9 - 5.3 3.1 2.1 - 4.1 Proportion of Three Dominant Species

(%)

6.1 5.3 - 6.9 4.7 3.3 - 6.1 Proportion of Fish as Benthic

Invertivores (%)

3.1 2.2 - 4.1 2.2 0.5 - 3.8 Proportion of Fish as Omnivores (%) 6.1 5.1 - 7.2 6.8 5.2 - 8.4 Proportion of Fish as Top Carnivores

(%)

2.8 1.8 - 3.9 1.8 0.5 - 3.0 Proportion of Fish as Simple

Lithophilus Spawners (%)

2.1 1.4 - 2.8 0.9 0.3 - 1.4 Fish Assemblage Tolerance Index 3.7 3.0 - 4.4 3.9 2.3 - 5.6 Adjusted CPUE 3.1 2.2 - 4.1 2.7 1.4 - 3.9 Overall FIBI score 39.9 35.4 - 44.5 32.1 25.4 - 38.8

CPUE = catch per unit effort

Table 38. Mean score (0 to 10 possible) and 95% Confidence Interval (CI) for the Index of Biotic Integrity (FIBI) and 11 metrics scores for 10 reference sites (31 sampling events) and 12 randomly selected REMAP sites (12 sampling events) in Ecoregion 47F lacking stable riffles and abundant

occurring in the watersheds. Elevated fecal coliform detections occurred throughout the monitoring project, with elevated fecal coliform detections associated with both rainfall runoff and late summer low flow periods. High fecal coliform counts during high flow may be due to both contributions from distal sources and local sources, but low flow peaks in fecal coliform imply that sources are close to the monitoring sites. The best monitoring strategy would probably be a combination of an event- based sampling design with fixed interval sampling to detect watershed-scale fecal coliform trends.

However, it is quite possible the monitoring program implemented during the project was sufficient to detect changes in fecal coliform if they in fact occurred. Statistically significant changes were observed in smaller subbasins where changes in pasture intensity were evident. Increases in fecal coliform in Walnut Creek subbasins may be due to bison grazing whereas a decreasing trend in upstream Walnut Creek and one Squaw Creek subbasin may be due to decreasing grazing activity. Overall, at a watershed scale, minimal changes occurred in grazing intensity or manure applications in

either Walnut or Squaw creek watersheds to expect measurement of statistically significant changes at their watershed outlets. Moreover, in the case of WNT2, a large pasture with cattle access to Walnut Creek is located within a half-mile of the downstream gaging station that probably limited the detectability of changes in fecal coliform concentrations in the Walnut Creek watershed.

Other studies have had success in documenting the effectiveness of BMPs to reduce sediment, nutrients and bacteria runoff from unrestricted livestock grazing (Meals, 2001; Line and Jennings, 2002; McNeil, et al., 2003). However, detecting changes in these NPS pollutants has typically required a sampling effort specifically designed to detect the change, including event-based sampling and before/after treatment comparisons. Thus, should future targeting of BMPs for pasture sites in Walnut and Squaw creek watersheds be considered, monitoring activities should be focused on isolating the change to a smaller area with an emphasis placed on designing an appropriate monitoring strategy.

In terms of phosphorus, data from the Walnut Creek project provides much needed information on concentration ranges and temporal patterns of P in small agricultural watersheds. However, like fecal coliform, a sampling strategy designed to capture P variability during both runoff events and baseflow would probably be needed to detect changes in P over time. Furthermore, additional analysis of total P and dissolved P (orthophosphate) in stream water would aid interpretation of P patterns and sources.

Detecting Changes in Biological Indices