Intermittent rivers and ephemeral streams are common flowing waters on Earth, but their ecological processes are still poorly understood in the Neotropical region. Temporal flow cessation leads resident communities of aquatic taxa to be constantly rearranged. Typically, diversity in intermittent systems is modulated by environmental and physical distance, however, this could change in humid regions with non-temperate seasonality. Here, we implement a metacommunity approach, to explore the influence of local and regional factors in structuring the composition and spatial variability of freshwater fish communities in a Neotropical biome. For this, we monitored the Cube River, an intermittent basin located in the last forests of Northwestern Ecuador within the Chocó Bioregion. Fish and environmental variables were sampled during the wet and dry seasons of 2021. Our results indicate that although local environmental variables differed between seasons, fish community composition did not change. However, fish density, biomass, trophic groups and fish community composition changed between seasons when considering fish diversity across sites with different eco-hydrological conditions. Some species, due to their adaptations and habitat preferences, were indicative of sites exhibiting intermittency in headwaters, whereas other were indicative of downstream sites. Metacommunity analysis showed that, in both seasons, community dissimilarity was significantly correlated with environmental distance, but not strongly with physical distance. Community dissimilarity exhibited a positive correlation with physical distance only for species with low dispersal ability. Our findings in the Chocó bioregion confirm and contrast previous hypotheses, in which, fish community were determined by environmental distance, where environmental filtering acts as the main driver of change in these intermittent river networks.