A central component of predictive ecology in wetlands is the analysis of species distribution as a function of their biotic and abiotic environment. This analysis is normally used by decision-makers in biodiversity conservation, species monitoring and environmental planning, among others. Habitat suitability modelling is a major component of the process of making the analysis, however, temporal and spatial variations of hydrological, hydrodynamic and environmental variables are normally not well known and overall values are assumed. In Abras de Mantequilla wetland (Ecuador) we find a tropical situation where the hydrodynamics of inflows seem to play an important role on the stability of the ecosystem. The habitat suitability in wetlands is driven by hydrodynamic, physical and biological interactions that are not fully understood. This research explores the habitat changes in space and time of a fish community in this tropical wetland, identifying extremes using constant habitat index (thresholds in a range) and one variable index (fuzzy rules) and a fuzzy combinations of hydrodynamic model variables. The main goal was to quantify the extension of the habitat areas were the index was high enough to be considered as suitable habitat, based on the hydrodynamic features and on spatio-temporal changes in the habitat index. The hydrodynamic variables water depth and velocity were modelled with DELFTFLOW software. A change of spatial distribution of the habitat for this group is related to the velocity and water depth. Results from the habitat model determined that the peak of the wet season was the period with a higher percentage of suitable areas for this fish assemblage, given the hydrodynamic variables selected. Thus, it would appear that the habitability of the Characidae in the littoral area is reduced when low flows occurred. Despite this fact, it is essential to acknowledge that other physical, chemical and biotic variables may play an important role in the presence of this community and therefore should be gradually included in future studies for an integrated ecological habitat assessment.