We investigated the impact of sewage discharge on Posidonia oceanica meadows in Mahdia, eastern Tunisia. We specifically addressed changes in biometric plant parameters and epiphytic microalgae composition on leaves caused by this anthropogenic interference. A hierarchical sampling design was used to compare epiphytic microalgae structure between one disturbed and two control stations. Samples were collected by SCUBA diving at 8 m depth in August 2009. A total of 58 microalgae taxa were identified on leaves. At the disturbed station, leaf length, leaf surface area and the leaf area index decreased, whereas epiphytic dinoflagellate abundances increased compared with the control stations, with more Prorocentrales, Protoperidiniales and potentially toxic species on leaves of the disturbed station. Moderate nutrient enrichment (mainly Si(OH)4 and NH4+) and low water transparency at the disturbed station were associated with the increased abundances of some dinoflagellate species.