Coastal nutrient loading is a primary driver of changes to habitat structure, species diversity, and increases in hypoxia and harmful algal blooms in estuaries worldwide. The difficulty of identifying non-point source inputs of nutrients often hinders the management and mitigation of these nutrient loads. Using stable isotopes, this study aimed to determine the primary sources of nutrients influencing the coastal Everglades, specifically lake systems in the rim of north-central Florida Bay. Carbon, nitrogen, and sulfur stable isotope values of algae grown in situ were used as a natural tracer of nutrient sources across hydrologic seasons (wet and dry seasons of 2021-2022), and across a north to south estuarine gradient in these coastal lake systems. Mean δ15N values (+2 to +3‰), consistent across both space and time, provided evidence that allochthonous N may primarily influence this region. Mixing models identified a mixture of upstream marsh and downstream bay derived nutrients primarily influencing the nutrient regime of the systems. Nutrient inputs varied with season and location. We observed higher marsh derived nutrient inputs in the upper portion of the system during the wet season, and greater nutrient inputs from Florida bay during the dry season, primarily in the lower portion of the estuary. This study highlights how managed restoration in marsh waterflow may increase N inputs, however, ecosystem-wide shifts must be better understood to predict ecological changes.