The Sacramento-San Joaquin Delta (the Delta) receives high loads of the nutrients nitrogen (N) and phosphorous (P) from wastewater treatment effluent and agricultural runoff. Flows from the Sacramento River, San Joaquin River, and other tributaries transport these loads through a complex network of rivers, channels and flooded islands, before entering San Francisco Bay.

Excessive loads of N and P can adversely impact ecosystem health by causing excessive algal blooms and low dissolved (Valiela et al, 1992; Kamer and Stein 2003). Excessive nutrients may also contribute to the occurrence of harmful algal blooms (Bates et al, 1989) and overgrowth of nuisance aquatic macrophytes (Valiela et al, 1992). Major nutrient management decisions are being considered in both the Delta and San Francisco Bay, and those decisions require the best-available science to understand the factors that regulate ambient conditions, and the effects of loads and ambient conditions on ecosystem health. A mechanistic and quantitative understanding of nutrient cycling and fate in the Delta is essential both for informed decisions related to current conditions and also because of major anticipated changes in both loads to the Delta (upgrades at wastewater treatment facilities) and habitat function due to restoration efforts and water management.

We hypothesized that the Delta is an important biogeochemical reactor, and that transformations or losses strongly regulate ambient nutrient concentrations within the Delta and modulate nutrient loads to San Francisco Bay. Both N and P have complex cycles and require careful investigation. In this paper, we focus on nitrogen, including loads, cycling, and losses or transformations that influence its ultimate fate.