This study focuses on the Mamanguape River in Northeast Brazil to investigate how environmental conditions influence fish assemblages within a metacommunity framework, offering insights into ecological dynamics that are broadly applicable to freshwater systems globally. Surveys conducted across seasonal variations, in the Mamanguape River revealed that fish diversity was higher in downstream sections, while the number of rare species decreased during dry period. These findings highlight the pivotal role of environmental gradients such as altitude, water velocity, and dissolved oxygen in species distributions and their resilience to changing conditions. During wet periods, mass effects facilitated long-distance dispersal, allowing species to recolonize lower-quality habitats. However, environmental sorting remained a crucial factor, with species distributed according to the conditions they are best adapted to. This resulted in compositional differences among sections of the river, a pattern likely consistent in intermittent river systems worldwide. While some sites in the upper section dry out completely, the remaining lentic (ponding) habitats serve as essential refuges, supporting fish communities until conditions improve. Globally, intermittent river systems face increasing conservation challenges due to anthropogenic pressures such as water infrastructure projects and altered flow regimes. In the Mamanguape River, the Sao Francisco River Integration Project and the Acaua-Ara & ccedil;agi canal pose risks to the ecological balance by disrupting the natural intermittent river regime. This study emphasizes the urgent need for conservation measures to protect freshwater biodiversity in the Mamanguape River and other similar systems, highlighting the broader implications of mitigating the impacts of environmental changes on intermittent rivers worldwide.