Heavy nutrient loads in coastal waters often lead to excessive growth of micro- and macroalgal epiphytes on seagrass leaves, with varying effects on the underlying seagrasses. This study evaluates the photosynthetic performance, epiphytic biomass, and tissue nutrient content of two common tropical seagrasses, Cymodocea serrulata and Thalassia hemprichii, in two intertidal areas along the Dar es Salaam coast in the Indian ocean; Ocean Road (near the city centre, nutrient-rich) and Mjimwema (south of the centre, nutrient-poor). Epiphyte biomass was significantly higher at the nutrient-rich site, and epiphytes were associated with reduced photosynthetic performance in both seagrass species at both sites. Likewise, nitrogen and phosphorus tissue content was higher in both species at the nutrient-rich site than at the nutrient-poor site, further illustrating the documented difference in nutrients between the two areas. Epiphytic species composition on the seagrass leaves varied between seagrass species and between sites. Cymodocea serrulata had a higher number of epiphytic species at Mjimwema than at Ocean Road, while Thalassia hemprichii had more epiphytic species at Ocean Road than at Mjimwema. Our results indicate that seagrass photosynthetic performance, epiphytic biomass and nutrient content of the seagrass are influenced by nutrient gradients in the water.