Estuarine and coastal areas are often considered as hotspots due to their high diversity and ecological importance. However, communities living on those areas are often submitted to fishery and climate change pressures causing modifications on fish assemblages. French Guiana’s coastal shelf is characterised by warm waters with high turbidity and low salinity caused by the large river discharges from the Amazon and nearby estuaries. The high productivity of these areas supports fisheries and aquaculture activities. However, the structure and dynamics of coastal fish populations in French Guiana have seldom been studied. The aim of this study was to understand the effect of environmental conditions, as well as the influence of the coast and nearby estuaries on the spatio-seasonal variability of demersal fish communities living in shallow coastal waters (less than 20m depth). Data were collected from two fishing campaigns using a multi-filament drifting net during the rainy and dry season at 55 sampling stations along the coast. Results showed a high spatial patchiness and no clear seasonal pattern. Higher abundances and diversities were observed near estuaries where both marine and estuarine species were cohabitating. The high number of rare species and the aggregative behaviour recorded in this study suggest that those communities could be particularly affected by climate change, pollution and overfishing. In the light of increasing pressures expected in this area, new regulations and management programs should be developed to ensure food security and biodiversity conservation.