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Periodically flooded environments in the Amazon River basin are recognized as being highly productive because of their limnological dynamics and ecological heterogeneity. They also have been historically impacted by fishery activities, therefore being crucial ecosystems to be considered in small‐scale conservation policies. Previous studies, however, did not detect or assess significant or consistent positive effects of combinations between protected areas or environmental variables on ichthyofauna. Accordingly, the present study analysed the effects of fishery management (hereafter categorization of lakes) and environmental characteristics on the attributes of fish assemblages in 20 floodplain lakes (eight categorized as open access; 12 categorized as protected lakes) inserted in a legally protected area, the Reserva de Desenvolvimento Sustentável Piagaçu‐Purus (RDS‐PP) in the lower Purus River, Amazonas State, Brazil. The results of the present study indicated depth, surface area and lake categorization synergistically influenced the ichthyofauna of these floodplain lakes. It also suggests this influence should not be treated separately in management policies. It was concluded that the potential effectiveness of fishery management in floodplain lakes is closely related to small‐scale (i.e. local) interventions, with emphasis on the role of the lakes as a unit of effective management of ichthyofauna in floodplains. Furthermore, participatory decisions during the process of elaborating management plans for floodplain lakes should consider environmental attributes relevant to biological communities and traditional knowledge. [ABSTRACT FROM AUTHOR]