The stage height and the width of the weir were used to compute flow using a calibrated stage-flow relationship. Pressure measuring devices including Design Analysis H355 Smartgas bubbler systems or HOBO water level loggers were used to measure stage. Data were collected and recorded every fifteen minutes at all flow stations. The fifteen minute flow data were averaged by day to calculate the daily average flow. Water samples were collected at the inlet and outlet of the wetlands on the same day at approximately two week intervals during the study period. Field sampling consisted of collecting depth-integrated water samples and recording field conditions at sites within the study area using an YSI 6600 sonde . Sondes were calibrated before sampling and calibration was confirmed within twenty-four hours after the sampling event. Water samples were collected in glass 1000 mL bottles , 1000 mL HDPE Trace-Clean narrow mouth plastic bottles , 250 mL HDPE Trace Clean wide mouth plastic bottles , 16×100 mm pretreated chlorine free glass tubes , and 40 mL trace clean vials with PTFE septa in accordance with requirements for different lab analysis and volume requirements. All bottles were rinsed with sample water prior to collection of a depth-integrated sample. Samples were immediately stored at 4°C after sampling and transported to the lab on the day of sampling.Samples were received by the laboratory the same day they were sampled,hydroponic nft logged in and inspected for damage, and stored at 4°C until filtering and analysis.

All filtration and preservation of samples were completed within 24 hours. Samples were collected, preserved, stored, and analyzed by methods outlined in Standard Methods for the Analysis of Water and Wastewater , unless otherwise indicated. Total organic carbon and dissolved organic carbon were analyzed on a Teledyne-Tekmar Apollo 9000 by high temperature combustion according to SM 5310 B. Nitrate-nitrogen was quantified using the TL- 2800 ammonia analyzer made by Timberline Instruments . Soluble reactive phosphate-phosphorus was quantified in filtered samples by the ascorbic acid method adapted from SM 4500-P-E. Based on the results of this study, we can begin to envision possible scenarios for the implementation of treatment wetlands in the San Joaquin River Basin. The result of the combined wetland and microcosm studies suggest that 10 cm d-1 is a reasonable estimate of k for wetland soils in the study area. During this study in 2008, flows at Ramona Lake averaged 20,300 m3 d-1 entering a marsh of approximately 81,000 m3 and had an average measured inlet nitrate-nitrogen of 3.4 mg L-1 . There are currently no regulatory limits for nitrate in agricultural drainage. Previous studies suggested that 0.5 mg L-1 can be used as the critical concentration above which nuisance algae problem can occur . Based on this criterion, the wetland areas required for achieving target nitrate effluent concentrations of 0.5 mg L-1 was calculated using Eq. . The relationship between effluent nitrate-nitrogen concentration and wetland size for the Ramona watershed is shown in Figure 2-6. To reach an effluent nitrate concentration of 0.5 mg L-1 , the Ramona watershed would need an area of 51 ha , which is equivalent to increasing the current marsh size approximately 6 times. The marsh size would need to be increased 15 times to reach the same effluent quality with a single pond system. Growers are reluctant to relinquish land from crop production, so accommodation between riparian wetland expansion and economic vitality must be reached.

Ramona Lake receives drainage from over 2,000 hectares of farmland and an expanded pond-in-series treatment wetland would represent approximately 2.5 % of that area. Additionally, these wetlands do not necessarily need to be located on productive farmland, since there are lower-value riparian areas within the levees defining the San Joaquin floodplain that are down-gradient of the agricultural lands . Diversion of irrigation drainage through constructed wetlands before discharge to the San Joaquin River is being further evaluated as a water quality management option by irrigation and drainage districts in the San Joaquin Valley.The functionality of the study sites as riparian buffers was assessed using the California Rapid Assessment Method for Wetlands . CRAM is a scientifically defensible rapid assessment tool that was developed by an association of local, state, and federal groups and allows a field team to assess the overall health of a wetland system, ranging from the best to worst possible conditions for that type of wetland. Using CRAM, a suitable Assessment Area is determined for the type of wetland being assessed. Four main attributes, including buffer and landscape context, hydrology, physical structure, and biotic structure, are broken down into fourteen metrics which are then assigned a score based on four alternate conditions, from best to worst , depending on the wetland type. Scores are changed to numeric values added up and converted to a percentage score for each main attribute and averaged across attributes to determine the wetland’s overall score. Scores can range from 25% to 100%, with 100% representing a fully functional wetland. The buffer and landscape context score measures the ability of the wetland to handle stress from the surrounding area and consisted of the metrics: landscape connectivity, percent of Assessment Areas with buffer, average buffer width, and buffer condition. Hydrology score is a measure of hydroperiod, channel stability, and how connected the wetland is to the adjacent floodplain.

The study area is characterized by a Mediterranean climate, with hot dry summers and cool wet winters.All of the sites were dominated by crop irrigation runoff during the dry season. The water source score was low for all of the sites that were studied, as all of the sites had an impacted hydrology regime. However, the sites still receive natural inputs, such as storm runoff and groundwater seepage. Physical structure assessed the physical diversity of the environment, with a higher diversity promoting a greater number of habitat niches. Structural patch richness measured the number of physical features, which identified the potential habitat and complexity of the wetland. The list of patch types was dependent on the wetland type and was found in the CRAM manual . Biotic structure included living flora in a wetland and was a measure of species richness and abundance and the physical structure of the plant community. The plant community score included three sub-metrics: number of plant layers, number of co-dominant species, and percent invasion. Each plant layer consisted of plants of similar height that made up at least 5% of the possible growing area.The four sites showed temporal and spatial variation in observed bio-degradation rates. Under aerobic conditions, average half-lives of chlorpyrifos were 5 , 16 , 18 and 21 days for Hospital Creek, Ingram Creek, Ramona Lake and San Joaquin River National Wildlife Refuge respectively . For most of the sampling events, degradation rate of chlorpyrifos was highest in Hospital Creek sediments followed by Ingram Creek sediments . Typical chlorpyrifos degradation curves along with formation of its transformation product TCP are shown in Fig. 3-6 to Fig 3-9 for field sediments. At the end of 21 days, chlorpyrifos concentration decreased to less than 1% of its initial concentration in Hospital Creek sediments and about 20% of the initial chlorpyrifos was measurable as TCP. This value is in agreement with previous chlorpyrifos degradation studies conducted on soils,hydroponic channel where TCP accounted for 10% to 30% of the initial chlorpyrifos concentration . TCP concentration reached its peak value at the end of 7 days and did not further accumulate. This may be due to the fact that TCP is subject to degradation . It has been suggested that most of the chlorpyrifos degrading microorganisms are either capable of degrading TCP or can tolerate high TCP concentrations because TCP has antimicrobial properties and can suppress microbial activity if it accumulates . The rate of abiotic chlorpyrifos hydrolysis was 0.02 d-1 in deionized water at pH 7.2 and 30o C , which corresponds to a half-life of 36.5 days, and is consistent with previously reported data . The initial chlorpyrifos concentration decreased by about 25% in killed control flasks over 21 days. The rate of chlorpyrifos degradation in killed control flasks was 0.02 d-1 , not significantly different from the control flasks without sediment, suggesting that abiotic hydrolysis was the dominant mechanism for the observed chlorpyrifos loss in the killed controls. In addition to the analysis of first-order decay curves, first-order degradation kinetics was evaluated by plotting log-mean chlorpyrifos concentrations versus degradation rates . Experiments from 2010 were combined and it was determined that the chlorpyrifos degradation was first-order with respect to the log-mean chlorpyrifos concentration . The slope of the regression line gives an estimate of the average firstorder degradation constant kdeg for field sediments. The first-order degradation rate constants obtained from this analysis was in reasonable agreement with kdeg values obtained from the exponential decay curves . Chlorpyrifos degradation rates can vary widely in different soils with half-lives ranging from 10 to 120 days. Only a few studies have been conducted in sediments, and half-lives ranged from 20 to 24 days in urban stream sediments , 27 to 77 days in nursery recycling pond sediments , and 58 to 144 days in sediments from a constructed wetland . Half-lives obtained in this study were within the range reported in the literature except Hospital Creek and Ingram Creek sites, which had significantly faster degradation rates for most of the sampling events.

The large variation in half-lives observed in previous studies has been attributed to different environmental factors, such as soil type, soil pH, moisture content, temperature, and organic carbon content . Watersheds included in this study have similar cropping practices and sediment properties . Therefore, physical characteristics do not explain the wide range of observed degradation rates. The difference observed in degradation rates in this study may be related to the wet-dry cycle of the typical agricultural drains , which would allow aerobic conditions to prevail, whereas the wetland sites are permanently flooded systems with anaerobic sediments. Hospital and Ingram Creek sediments were typically light brown in color indicative of aerobic conditions whereas the wetland sediments were dark gray indicating reduced conditions. Agricultural drains typically have low flow rates and occasionally dry out during non-irrigation season in late fall and winter; however, high flows and flooded conditions were observed for Hospital Creek during sampling events in 2011 which may account for a consistent decrease in observed removal rates at this site compared to the previous year . To investigate the effect of redox potential on chlorpyrifos degradation, sediments with highest chlorpyrifos degradation capacity from Hospital Creek were incubated under anaerobic conditions. Chlorpyrifos degradation rate was much lower under anaerobic conditions . Half-life of chlorpyrifos in Hospital Creek sediments under anaerobic conditions increased to 92 days . The inhibitory effect of anaerobic conditions on chlorpyrifos degradation has been previously documented for soils and sediments . These results suggest that allowing a wet-dry cycle can enhance the degradation rates of an organophosphate insecticide in these systems by providing aerobic conditions in sediments. The application of a wet-dry cycle is a useful management tool for the rehabilitation of permanently flooded wetlands . The persistence of aquatic wetland plants during wet-dry cycle is ensured by regular reseeding of the population by seed germination . During dry phase, emergent plant species germinate on exposed mudflats and when water returns, they expand by vegetative propagation . Depth and duration of the flooding period will affect how these wetland communities develop. A long period under permanently flooded conditions is not desired both from the ecological point of view, as it would likely result in decreased plant species richness, and from a pesticide management point of view, as sufficient aeration is desired between consecutive irrigation seasons. The proposed wet-dry cycle period would be similar to agricultural drains in the region. The dry phase would encompass the non-irrigation season in late fall and winter, and the wetland would be flooded again in spring and summer when the irrigation season begins. In the dry phase, given the moderate volatility of chlorpyrifos, volatilization would not be a significant dissipation pathway unless spray applications occur. On the other hand, photolysis may contribute to chlorpyrifos degradation in dry sediments if it is exposed to direct sun light.