Connectivity is a key factor in metacommunity ecology, because it influences dispersal and colonization rates. However, it has received less attention in aquatic than in terrestrial ecology research. We investigated whether connectivity is a good predictor of species richness in functional fish communities (freshwater, FS; estuarine, ES and estuarine-freshwater, EFS) from 31 coastal lakes in southern Brazil. We used a model selection approach, including lake area and distance from the ocean as additional predictors of species richness and two connectivity metrics: primary connectivity (C P) and estuarine connectivity (C E), which measure connectivity to neighboring lakes and system-wide connectivity, respectively. Both metrics estimate functional connectivity and were calculated on habitat-based cost distances. Connectivity was more important for predicting richness of functional communities than for total richness, particularly C E, which was distinctively related to each functional fish community richness (directly related to ES and EFS, and inversely related to FS; C P was related only to ES). Remarkably, connectivity was more important than area for predicting ES and EFS richness. These results add support to dispersal limitation as an important mechanism influencing fish communities. We suggest that incorporating environmental filters (habitat type) to quantify connectivity is useful for accessing the patterns of species richness.