In many marine ecosystems small pelagic fish exert a crucial role in controlling the dynamics of the community, mainly due to their high biomass at intermediate levels of the food web. These fish use coastal marine ecosystems as nursery areas, but also to forage and to avoid predation or competition. We studied spatial, seasonal, lunar and diel variations in a coastal fish community from a marine protected area of the Bijagós Archipelago, Guinea-Bissau. Fish were sampled with 46 beach seine net sessions in 2015 and 2016. A total of 35 fish species of 25 families were captured. Fish abundance varied between years and seasons, with a higher abundance in the dry season, but not by lunar tide. Nonetheless, the community composition was broadly similar over the seasons, among islands and between lunar tides. Clupeidae, Haemulidae and Gerreidae were the most abundant fish families. Sardinella maderensis highly dominated the captures throughout the year, with catches much higher than any other species. The differences in abundance between seasons and years may be related with movements to or from the shore due to feeding activity or to avoid predation, or else to differences in recruitment between years. There were no significant diel differences in species richness and diversity, although higher numbers of fish were captured during daytime. For most species the majority of individuals captured were immature, highlighting the importance of the archipelago as nursery area for several species. These small pelagics, and particularly Sardinella maderensis, represent the main prey for several marine predators. Thus, the conservation of such fish species may be key for the management of the Bijagós Archipelago.