The Media Luna spring, Mexico, is the main reservoir of the endemic and endangered fish Ataeniobius toweri. In the last decades, the ecosystem has been modified by tourism, and the habitat has changed for this species. Therefore, for better conservation management of the natural fish population, it is necessary to understand its abundance status and suitable habitat conditions, in ecological and spatial scenarios, on a temporal scale. In the present study, we modeled A. toweri’s ecological responses and spatial distribution for adult and juvenile life stages, in three summer periods (years 1999, 2009, and 2019). As habitat variables, we used water depth and underwater coverage. Ecological response curves were obtained from a Generalized Linear Model; distribution models were obtained with DOMAIN. In the modeling evaluation, for the Linear Regression Model, we obtained true statistical skills metric > 0.30 and, for DOMAIN, an area under the curve (AUC) > 0.70 with an AUC ratio > 1.00. In general, as the summer periods progressed, we found the highest probability of occurrence (P > 0.20) and distribution (P > 0.60) in areas with conditions of large coverage of underwater vegetation, in the first 1.5 m of depth, and near the shores of the spring. Also, the variations of relative abundance were always observed at sites with these habitat conditions. Thus, we concluded that our models had the performance to discern between suitable and unsuitable habitat conditions for A. toweri, and that areas with little or no anthropogenic pressure are more important for this species.