In contrast, Watsonville Slough had its highest SRP concentrations from fall through spring, with concentrations declining to an annual low point in mid summer . High SRP concentrations in the winter rainy season may be associated with increased surface runoff from agricultural fields located along the slough. Tile drains may also facilitate subsurface loses of phosphorus . In Carneros Creek, which is dry from approximately May until December each year, a third seasonal pattern emerged . SRP concentrations were moderately elevated at both upstream and downstream sites following the first winter rains, which suggests that soil phosphorus accumulates over the summer months and is flushed into the creek with the first rains. At Dunbarton Road where there is little cultivation upstream, sources may include natural decomposition in grasslands, cattle grazing, and rural residential land use; at downstream sites sources also include agricultural land use. At San Miguel Canyon Road, the downstream location, SRP concentrations increased again in the late winter and spring of 2002 and 2003, reaching very high levels that frequently exceeded 1 mg/L. Nutrient concentrations were highly erratic in 2002 and 2003, and subsequently declined in 2004, suggesting that nutrients originated from a point-source that has ceased to discharge. No seasonal concentration trends were observed in the upstream tributaries of the Pajaro River . At these locations SRP concentrations remained low throughout the year. We calculated the SRP load discharged by each tributary ,procona buckets and found loads varied seasonally corresponding with discharge . The SRP load was greatest at Chittenden during January and February, when discharge was also greatest. San Juan Creek was not sampled during this period, but likely accounts for a significant portion of the unaccounted load because it has elevated SRP concentrations and year round flow. In the Pajaro River, there is a strong seasonal trend in SRP concentrations .

Concentrations decline after the rainy season ends. Because SRP concentrations remain relatively high in the winter, rainfall probably transports SRP to surface waters. Furthermore, the loss of SRP from Santa Clara/San Benito Counties is highest during these rainfall periods . Because concentrations and export of SRP in the Pajaro River are rainfall dependent, it is difficult to determine long-term trends independent of recent rainfall patterns.Elevated phosphorus concentrations can cause excessive algal growth in waterways, and preventing excessive growth is the primary reason phosphorus concentrations are regulated. Algal biomass in the water column can be determined from the concentration of chlorophyll a, which indicates the degree of excessive algal growth. We monitored chlorophyll a concentrations at several sites in the Pajaro River watershed on a biweekly basis and compared these concentrations to phosphorus. The lack of a direct correlation between chlorophyll a and phosphorus levels indicates that P availability is only one of the factors controlling algal growth. Canopy cover and turbidity , algae-eating organisms , substrates that allow different types of algae to attach, and algae sources also play a role in algal growth and chlorophyll a concentrations. Furthermore, additions of nitrogen can stimulate algal growth in streams and rivers, which challenges the commonly held belief that phosphorus is the nutrient that controls the growth of algae in freshwater ecosystems. Our research group from the Center for Agroecology and Sustainable Food Systems has begun efforts to assess the growth patterns of algae in order to determine how elevated phosphorus and nitrogen levels influence these patterns. Under state legislation known as the Agricultural Discharge Waiver that took effect in January 2005, farmers are required to develop farm water quality plans to protect surface waters along the Central Coast. One goal of our research is to inform growers of current water quality conditions in waterways adjacent to their land so that they can take steps to reduce their impacts on waterways while continuing to farm profitably. Because phosphorus is transported to waterways in storm and irrigation runoff, reducing soil erosion and surface runoff is an important step in reducing phosphorus losses from the farm .

Subsurface flow is also an important mechanism of phosphorus losses from the farm . Growers can address these losses by matching P demand in plants with fertility management, keeping P concentrations in soils at agronomically responsive levels , and managing irrigation to minimize or eliminate runoff. It is important to note that many growers on the Central Coast and throughout the state have already initiated practices to reduce the loss of phosphorus from their farms. The University of California has several research projects in progress to document the impacts of changes in farm management, and a number of government agencies and NGOs are working with growers to improve water quality .Despite growers’ efforts, the target level of 0.12mg/L or lower for ortho-P set by the RWQCB may be difficult to attain in the lower Pajaro River and Elkhorn Slough watersheds, where natural sources of phosphorus may be high, and tile drainage systems facilitate losses of phosphorus to surface waters. Even with changes in agricultural practices, the ambient water quality improvements may not be detected for several years, which makes enforcing the water quality regulations difficult on the short-term. Thus, long-term monitoring programs are important to determine the success of changing management practices.Nitrate contamination of freshwater resources from agricultural regions is an environmental and human health concern worldwide . In agriculturally intensive regions, it is imperative to understand how management practices can enhance or mitigate the effect of nitrogen loading to freshwater systems. In California, managed aquifer recharge on agricultural lands is a proposed management strategy to counterbalance unsustainable groundwater pumping practices. Agricultural managed aquifer recharge is an approach in which legally and hydrologically available surface water flows are captured and used to intentionally flood croplands with the purpose of recharging underlying aquifers . AgMAR represents a shift away from the normal hydrologic regime wherein high efficiency irrigation application occurs mainly during the growing season. In contrast, AgMAR involves applying large amounts of water over a short period during the winter months. This change in winter application rates has the potential to affect the redox status of the unsaturated zone of agricultural regions with implications for nitrogen fate and transport to freshwater resources.

Most modeling studies targeting agricultural N contamination of groundwater are limited to the root zone; these studies assume that once NO3 – has leached below the root zone, it behaves as a conservative tracer until it reaches the underlying groundwater or, these studies employ first order decay coefficients to simplify N cycling reactions . However, recent laboratory and field-based investigations in agricultural systems with deep unsaturated zones have shown the potential for N cycling, in particular denitrification, well below the root zone . For example, Haijing et al. found denitrifying enzyme activity as deep as 12 metersin an agriculturally intensive region in China. Lind and Eiland reported N2O production in sediments taken from 20 meter deep cores. Other studies have reported the capability of deep vadose zone sediments to denitrify in anerobic incubations with or without the addition of organic carbon substrates . Moreover,procona florida container in agricultural settings, especially in alluvial basins such as in California with a history of agriculture, large amounts of legacy NO3 – has built up over years from fertilizer use inefficiencies and exists within the deep subsurface . It is not yet clear how this legacy nitrogen may respond to changing hydrologic regimes and variations in AgMAR practices, and more importantly, if flooding agricultural sites is enhancing nitrate transport to the groundwater or attenuating it by supporting in situ denitrification. Denitrification rates in the subsurface have been reported to vary as a function of carbon and oxygen concentrations, as well as other environmental factors . While total soil organic carbon typically declines with depth , dissolved organic carbon can be readily transported by water lost from the root zone to deeper layers and can therefore be available to act as an electron donor for denitrification . Oxygen concentration in the vadose zone is maintained by advective and diffusive transport, while oxygen consumption occurs via microbial metabolic demand and/or abiotic chemical reactions . The effects of drying and wetting cycles on oxygen concentrations in the deep subsurface are not well documented. However, in 1 meter column experiments, there is some evidence that O2 consumption proceeds rapidly as saturation increases and rebounds quickly during dry periods . These variations in oxygen concentration can influence N cycling and thus, transport to groundwater. Variability in nitrate concentration has also been linked to heterogeneous subsurface properties, rainfall events, seasonality of flow and other local geochemical conditions across a diversity of settings However, a gap currently exists in quantifying N attenuation and transport from agriculturally intensive regions with a “deep” vadose zone while accounting for the many competing N cycle reactions and transformations, as impacted by different hydrological regimes imposed under AgMAR.

The application of AgMAR itself can vary in terms of the hydraulic loading and rates used, as well as the duration between flood water applications. These can in turn affect water retention times, O2 availability, consumption of electron donors and consequently, denitrification rates . For example, denitrification rates were found to increase with increased hydraulic loading and with shorter times between flood applications within the vadose zone of a rapid infiltration basin system used for disposing of treated wastewater . In shallow, sandy soils, high flow rates – above an infiltration threshold – were negatively correlated with denitrification rates, suggesting that an optimum infiltration rate exists for a given sediment stratigraphy to maximize NO3 – reduction . Given the immense stratigraphic heterogeneity in alluvial basins, such as in California’s Central Valley, a range of optimum infiltration rates may exist with implications for managing AgMAR differently based on the geologic setting of the intended site. Therefore, the objectives of this study are to: a) understand the effects of varying stratigraphy and hydrologic regimes on denitrification rates, and b) identify AgMAR management scenarios that increase denitrification rates, such that the potential for N leaching to groundwater is decreased. Herein, we focus on an agricultural field site in Modesto, California located within the Central Valley of California, which is responsible for California’s $46 billion-dollar agricultural economy . The field site typifies the deep vadose zones prevalent in this region, which are characterized by heterogenous layered alluvial sediments intercalated with discontinuous buried clay and carbon rich paleosols . These discontinuous, layered features, especially the paleosols and areas of preferential flow, are typically associated with enhanced biogeochemical activity, higher carbon content and availability of metabolic substrates such as nitrogen . These regions respond to and change depending on environmental conditions such as water content and oxygen concentration in situ that are influenced by the hydrologic regime at the surface and may be important for NO3 – attenuation and reduction prior to reaching the water table. Therefore, this study considers varying hydrologic regimes and stratigraphic variations that are prevalent in the region. More specifically, at the Modesto field site , large amounts of legacy N already reside in the vadose zone, while N fertilizer application and irrigation occurs throughout the spring and summer months. AgMAR, if implemented, occurs during the winter months as water becomes available. Therefore, we focus here on quantifying the effects of AgMAR on N cycling in the deep vadose zone and implications for NO3 – contamination of groundwater at this characteristic agricultural field site. We also investigate the specific AgMAR application rates that would increase the effectiveness of in situ denitrification under different stratigraphic configurations through the development and testing of a reactive transport model. We believe such an analysis provides important insights for the successful application of AgMAR strategies aimed at improving groundwater storage in a changing climate. Reactive transport models can be beneficial tools to elucidating N fate and transport in deep vadose zone environments. Herein, we develop a comprehensive reaction network incorporating the major processes impacting N transport and attenuation, such as aqueous complexation, mineral precipitation and dissolution, and microbially mediated redox reactions. While using the same reaction network, we implement several numerical scenarios to quantify the range of denitrification rates possible under different AgMAR implementation strategies and stratigraphic configurations . For the latter, we used four different stratigraphic configurations with a low permeability layer on top including i) two homogeneous textural profiles, ii) a sand stratigraphy with a discontinuous silt band, iii) a silt stratigraphy with a discontinuous sand band, and iv) a complex stratigraphy more representative of the field conditions investigated by electrical resistance tomography .