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This study aimed to evaluate whether the upper São Francisco River basin floodplain is still used as a nursery by migratory fish and present the current status of the area’s ichthyofauna after almost 40 years since the only survey was conducted in the region.

Sampling occurred in seven perennial lagoons and six temporaries from São Francisco River or its direct tributaries using gillnets and trawls. Temperature, pH, and transparency of each lagoon were measured. The estimated richness was calculated, and the fish assemblage from both perennial and temporary lagoons was compared using NMDS and ANOSIM.

Forty species were captured, of which four were non-native and three were migratory. Although there was a low abundance of migratory species, most captured individuals were juveniles. Moreover, the perennial lagoons showed higher species richness.

After almost 40 years, the floodplain lagoons of the upper São Francisco basin remain important for the recruitment of migratory species and harbor an impressive proportion of fish fauna in the upper São Francisco area. However, the reduction of migratory species and the presence of non-natives may be a sign of the degradation of these environments, emphasizing the need for conservation measures in this area.