River deltas and their diverse array of aquatic environments are increasingly impacted by anthropogenic inputs of nitrogen (N). These inputs can alter the N biogeochemistry of these systems and promote undesirable phenomena including harmful algae blooms and invasive aquatic macrophytes. To examine N sources and biogeochemical processes in the Sacramento-San Joaquin Delta, a river delta located in central California, USA, that is fed primarily by the Sacramento River, we utilized a multi-tracer approach that measured N species concentrations and stable isotope values monthly from April 2011 to November 2012 in samples collected from the channelized mainstem of the Sacramento River, two channelized distributaries of the Sacramento River, and the Cache Slough Complex, a network of Sacramento River tributaries and shallow water wetland habitat. We found that the Sacramento River and its channelized distributaries received N primarily in the form of NH₄⁺ from treated wastewater effluent and that NH₄⁺ was lost rapidly while NO₃⁻ was gained more slowly during subsequent downstream transit, driven by an array of biogeochemical processes whose identities could be constrained via examination of stable isotope values. The Cache Slough Complex, which was characterized by lower net flows and higher water residence times than the Sacramento River and its distributaries, received variable inputs of low conductivity water elevated in NH₄⁺ from the Sacramento River and higher conductivity water elevated in NO₃⁻ from landward tributaries. Deviations from expected conservative mixing of these sources were spatially variable but broadly indicative of local inputs of treated wastewater effluent NO₃⁻, conversion of Sacramento River NH₄⁺ to NO₃⁻ via nitrification, uptake of NH₄⁺ and NO₃⁻ by phytoplankton, and remineralization of organic N. These findings highlight both the diversity in N dynamics in anthropogenically impacted river delta environments and the utility of a multi-tracer approach in constraining these processes in such complex systems.