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Knowledge about the diversity and spatiotemporal variability of epiphytic diatom communities in estuarine meadows has great relevance for coastal ecology and, thus, contributes to understanding the impact of natural and anthropogenic changes on seagrass meadows. The community of epiphytic diatoms in <i>Ruppia maritima</i> L. meadows was investigated in two environments with different levels of anthropogenic impact and nutrient loads. Both impacted and non-impacted meadows had similar conditions in terms of water depth, temperature and transparency but distinct nutrient loads and salinity ranges. A total of 159 diatom taxa were found on <i>Ruppia maritima</i> leaves during the monitoring period, including freshwater (30.8%), marine (25.1%), brackish (9.4%) and cosmopolitan (8.8%) taxa. The most abundant species were <i>C. placentula</i>, <i>T. tabulata</i>, <i>M. pumila</i> and <i>T. fasciculata</i>, in addition to <i>A. tenuissimus</i>, <i>C. adhaerens</i> and <i>M. moniliformis</i>. Although present in both sites, <i>C. placentula</i> and <i>T. tabulata</i> were the dominant species in the impacted site. We found that 32% of the taxa were exclusive to the non-impacted site, 23% to the impacted site and 45% were common to both sites. The study sites showed marked differences in community attributes; i.e., higher richness, diversity and equitability and lower dominance were found in the non-impacted site, which is distant from anthropogenic sources of domestic and industrial sewage and has low concentrations of dissolved N and P in water and low values of sediment organic matter. Nutrient concentration and salinity were the main factors behind the spatial and temporal variability in the structure of the epiphytic community when all other environmental variables were similar (water depth, temperature, transparency and host plant). The influence of temperature and salinity on community structure was site-dependent. This study revealed the high richness and diversity of epiphytic diatoms in the meadows of the Patos Lagoon estuary (PLE) and the high spatial and temporal heterogeneity of the communities, and it shows the potential of epiphytic community studies for the assessment of environmental quality in seagrass meadow habitats.