Urban sprawl poses a major threat to aquatic biodiversity. The species richness in fish assemblages of fifteen ecosystems with different degrees of hydraulic connectivity in the floodplain of the Grijalva River watershed has been analysed and described along five years. After human interventions, four lagoons are permanently disconnected and three are temporarily connected. The other three lagoons stay permanently interconnected. Native cichlids and poeciliids dominated in number of species, representing 24 of the 55 listed species. These 55 species include six non-native invasive species in the Usumacinta Province. The lowest number of species was recorded in urban lagoons, while they were similar in rural lagoons and rivers. In addition, 60% of the fish absent in the lagoons of the Metropolitan Area of Villahermosa (MAV) are species with a marine or an estuarine affinity; thus, the permanently disconnected MAV lagoons have seven species less than the permanently connected rural lagoons. Diversity corresponds to that reported in the literature. In urban lagoons, low diversity and the high percentage of lacking fish with a marine or an estuarine affinity indicate that ichthyological diversity is favoured by the interconnection of rivers and rural lagoons in the floodplain of the Grijalva River Basin.