Septic systems located near coastal waterways can contribute to nutrients that lead to eutrophication, harmful algal blooms, and high levels of fecal coliforms such as E. coli. This study defines pathways and timescales of nitrogen transport released from septic systems using a groundwater-flow and nitrogen transport model of a coastal subdivision connected to 2,000 septic systems and dissected by a dense network of canals. Lift station effluent data are used as a proxy to quantify average household septic nitrogen and fluid contributions of 11 kg/year and 160 m³/year, respectively. These fluxes are upscaled and applied to five sewer conversion zones, each having a known number of septic systems. Model results provide a basis for assessing nitrogen transport timescales associated with (1) coastal groundwaters for regions with high septic density near the coastline and (2) groundwater–canal interaction. Timescales associated with nitrogen removal by natural groundwater flow in a sandy surficial aquifer, following septic to sewer conversion, are predicted by the model to be on the order of 2–3 years for 50% reduction and 8–10 years for 90% reduction. Both numerical and collected field data indicate that canals significantly influence groundwater flow and have the potential to convey nitrogen to coastal waters at rates several orders of magnitude higher than introduced by submarine discharge along the coast. Pre and post sewer conversion data on nitrate and total nitrogen in shallow groundwater from a nearby field site, obtained post-model development, support the nitrogen concentrations and timescales predicted by the numerical model.