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Abstract Miami‐Dade County (MDC) has over 112,000 septic systems, some of which are at risk of compromise due to water table rise associated with sea level rise. MDC is surrounded by protected water bodies, including Biscayne Bay, with environmentally sensitive ecosystems and is underlain by highly transmissive karstic limestone. The main objective of the study is to provide first estimates of the locations and magnitudes of septic return flows to discharge endpoints. This is accomplished by leveraging MDC's county‐scale surface‐groundwater model using pathline analysis to estimate the transport and discharge fate of septic system flows under the complex time history of groundwater flow response to pumping, canal management, storms, and other environmental factors. The model covers an area of 4772 km²in Southeast Florida. Outputs from the model were used to create a 30‐year (2010 to 2040) simulation of the spatial–temporal pathlines from septic input locations to their termination points, allowing us to map flow paths and the spatial distribution of the septic flow discharge endpoints under the simulated conditions. Most septic return flows were discharged to surface water, primarily canals 52,830 m³/d and Biscayne Bay (5696 m³/d), and well fields (14,066 m³/d). Results allow us to identify “hotspots” to guide water quality sampling efforts and to provide recommendations for septic‐to‐sewer conversion areas that should provide most benefit by reducing nutrient loading to water bodies.