Effluent from septic systems can pollute groundwater and surface waters in coastal watersheds. These effects are unknown for the highly urbanized central Indian River Lagoon (CIRL), Florida, where septic systems represent > 50% of wastewater disposal. To better understand these impacts, water quality was assessed along both canals and a tributary that drain into the CIRL. Dissolved nutrient concentrations were higher near septic systems than in natural areas. δ¹⁵N values of groundwater (+7.2‰), surface water (+5.5‰), and macrophytes (+9.7‰) were within the range for wastewater (>+3‰), as were surface water concentrations of the artificial sweetener sucralose (100 to 1700 ng/L) and fecal indicator bacteria density. These results indicate that septic systems are promoting eutrophication in the CIRL by contributing nutrient pollution to surface water via groundwater. This study demonstrates the need to reduce reliance on septic systems in urbanized coastal communities to improve water quality and subsequently mitigate harmful algal blooms.