Inventorying nutrient and trace element sources in the Sacramento-San Joaquin Delta (the Delta) is critical to understanding how changes—including alterations to point source inputs such as upgrades to the Sacramento Regional Wastewater Treatment Plant (SRWTP) and landscape-scale changes related to wetland restoration—may alter the Delta’s water quality. While island drains are a ubiquitous feature of the Delta, limited data exist to evaluate island drainage mass fluxes in this system. To better constrain inputs from island drains, we measured monthly discharge along with nutrient and trace element concentrations in island drainage on three Delta islands and surrounding rivers from June 2017 to September 2018. These data were used to calculate island-level fluxes and then upscaled to estimate Delta-wide contributions from island drains. Based on these results, we present (1) new estimates of gross and net nutrient and trace element fluxes from Delta island drains, and (2) concomitant N stable isotope data to improve our understanding of island N cycling. Over 60% of nearly all island drainage gross nutrient and trace element loads occurred in winter and spring. Upscaled island drainage net annual total nitrogen (TN), total dissolved nitrogen (TDN), and NH4+ loads comprised an estimated 9%, 7%, and 4%, respectively, of annual inputs to this system in 2018, before the SRWTP upgrade. Under a post-upgrade scenario, we estimated net annual island drainage TDN contributions to increase to 11% and NH4+ contributions to 45% of total Delta inputs as the SRWTP NH4+ load diminished to near zero. Our results suggest that island drainage is a measurable N source that has likely become increasingly important now that the SRWTP upgrade is complete. With over 200 potential active outfalls, these inputs may affect aquatic biogeochemical cycling in many regions of the Delta, especially in areas with long residence times.