The physicochemical variables and the ichthyofauna associated with aquatic macrophyte beds in two stretches of the baía Caiçara were evaluated seasonally between September 2005 and May 2007. Low depth, high water transparency, and relatively well-oxygenated waters characterized both stretches during the low water season, whereas the flooding of the upper Paraguay River correlated with drastic alterations in these variables: depth registered a fivefold increase, and turbid and anoxic waters predominated during the high water season. During the falling and low water seasons, species richness, fish abundance, biomass, and diversity were significantly higher than during periods of rising and high waters. The presence of large-sized migratory species, however, was strictly associated with the high water season. The results suggest strong relationships between the abiotic and biotic components of the system and indicate an overall high degree of dependence of the system on the hydrological seasonality of the upper Paraguay River.