Disentangling multilevel sources of variation is critical for understanding of diversity patterns in high-variability environments. We investigated the scale sensitivity of short-term environmental effects on the temporal beta diversity of fishes in 3 tropical coastal lagoons in Southeastern Brazil. Environmental effects were investigated at 3 hierarchical levels (local, zone, and lagoon). An AICc-based model selection was applied to generalized linear mixed models relating abundance-based beta diversity (Bray-Curtis dissimilarity; βBC) to environmental distances and random effects for other sources of variability. Abundance gradients (βBC-GRA) contributed more for βBC at all hierarchical levels, most likely due to random changes in the abundances of numerous rare marine-origin species. The temporal and spatial marine influences favored the balanced variation in the abundance of different species (βBC-BAL), probably by allowing for marine species with different environmental tolerances and requirements. The freshwater vs. marine influences were primarily represented by short-term effects of salinity changes at the local and zone levels and tide height and accumulated rainfall at the lagoon level. Other environmental effects (e.g. pH and transparency) were representative of that balance depending on the βBC component and hierarchical level. Random effects for morphometric features (local level, width of the connections between zones; lagoon level, distance from the ocean) and climate-related factors (local and zone levels, wind intensity and accumulated rainfall; lagoon level, changing seasons) were also relevant for the relationships between environmental variability and βBC. This study evidenced major scale-related mechanisms driving the temporal beta diversity of fishes in tropical coastal lagoons.