Coastal river deltas are often altered for human needs, straining ecosystems. The Sacramento-San Joaquin River Delta (Delta) in California exemplifies this with dense human population, agricultural modification, and engineered flows. These modifications have been associated with declines in phytoplankton and a subsequent collapse in pelagic fish species in the Delta. One hypothesis to explain the phytoplankton decline suggests, paradoxically, that ammonium concentrations are too high. The premise is that ammonium can inhibit nitrate uptake by phytoplankton, altering phytoplankton communities and reducing gross primary production. Historically, the main point source of ammonium to the Delta was the Sacramento Regional Wastewater Treatment Plant (SRWTP). However, treatment plant upgrades completed in April 2021 have essentially removed ammonium from the effluent and increased nitrate concentrations, potentially bolstering primary production. Our study investigates the spatial extent to which ammonium and nitrate concentrations have changed in the Delta following the SRWTP upgrade and if there has been a detectable response in primary production. We have collected discrete and continuous water quality data for ammonium, nitrate, nitrite, and chlorophyll-a throughout the Sacramento-San Joaquin Delta at 11 sites in the four years preceding and three years following the 2021 SRWTP upgrade. Across the length of the study, all sites experienced increased nitrate in the fall, and all but one site had lower nitrate in the spring. Following the upgrade, multiple sites proximal to the SRWTP exhibited lower ammonium concentrations. Nevertheless, preliminary findings using multivariate autoregressive state space models found that changes over time in ammonium and nitrate concentrations were associated temporally with seasonal variation to a greater degree than the timing of the upgrade. No significant change in algal biomass was detected. Our preliminary findings suggest that any biotic changes resulting from reductions in wastewater nutrient supplies may take longer to materialize than anticipated, if they do occur.