Mangroves are of great ecological and socio‐economic importance, yet they are under threat from urban development on the southern Pacific coast of Costa Rica. To test for possible nutrient‐related impacts, we compared water‐column nutrient concentrations, C and N stable isotope values and other environmental variables between mangroves with known sewage loading (three “nutrient loaded” locations) and those without such loading (three “reference” locations). Instantaneous nutrient concentrations were low at all locations, Secchi depth was greater at reference locations, and chlorophyll concentrations were higher at nutrient loaded mangroves. Suspended matter did not vary between reference and nutrient loaded mangroves, and nor did bivalve and algal δ¹³C and δ¹⁵N values. Enrichment of δ¹⁵N and δ¹³C of red mangrove leaves at the nutrient loaded locations is attributed to pulsed inputs of materials that were not detected in the instantaneous nutrient data. We provide evidence of isotopic enrichment at nutrient loaded locations from mangrove material and recommend that adequate waste water treatment be carried out on all anthropogenic discharges into this vulnerable marine system.