Spatial and temporal variation of the physical and chemical conditions of coastal karst wetland ecosystems, which annually range from flooded to completely dry, generate a very dynamic fish community structure. We assessed the relative influence of spatial dependence and environmental factors on fish community structure in a seasonally flooded tropical karst system on the north-western coast of the Yucatan Peninsula, Mexico. Sampling was carried out between November 2009 and April 2010, while the area was inundated by seasonal floodwater. Fish biomass, abundance and species richness, as well as environmental variables and geographic location, were recorded. A variation partitioning analysis was performed to assess the influence of the spatial and environmental variables on the fish community using multiple regression, and a principal coordinates analysis of neighbor matrices (PCNM). Spatial factors had a greater influence on the changes in the community structure than the environmental factors. After spatial variation, environmental effects from conductivity, oxygen saturation, temperature and depth further shaped the community. These results imply that, despite the diversity of niches and wide variation in environmental conditions, the structuring force of the community is the spatial dynamic probably linked to species dispersal mechanisms and reproductive strategies.