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Context: The replacement of native vegetation by exotic grasses for livestock production is driving landscape homogenization, habitat fragmentation and reducing connectivity between habitat patches in floodplains ecosystems. Objective: In this context we examined how changes in native and exotic vegetation cover, connectivity and water depth affect the attributes of the small [standard length (SL) < 80 mm as adults] and large-sized fish assemblages (SL ≥ 80 mm as adults). Method: We assessed the effects of water depth, exotic and native vegetation cover and habitat connectivity on the abundance, species richness, body size and biomass of fish assemblages in a 25 km area of the seasonal habitats of the Pantanal wetland over 5 years. Results: We showed that fish assemblage response to meso-scale variation in water depth, vegetation cover and habitat connectivity in seasonal habitats is size-dependent. The gradient from exotic to natural vegetation cover did not affect the assemblages of small-sized fish, which were mostly regulated by water depth, habitat connectivity and the gradient from grassland to forest. However, besides being affected by water depth and habitat connectivity, large-sized fish were also affected by the gradient from exotic to natural vegetation cover. Conclusion: Our results indicate that transformations in the landscape and changes in the dynamics of inundation may have negative consequences for the long-term persistence of fish assemblages in the Pantanal wetlands. [ABSTRACT FROM AUTHOR]