The study of the coexistence of three closely related species ( Chirostoma consocium, C. jordani and C. labarcae) in the fluctuating environment of Lake Chapala, Mexico, was developed to delineate elements for management and conservation. First, we genetically categorized (RAPD-PCR and mitochondrial sequences) the species to corroborate their identity. Phylogenetic relationships suggested the presence of three different clades where each of the species belonged (separation between and within guilds). Second, we functionally categorized the species by analyzing trophic ecology. Important interactions between guilds occurred because piscivorous Chirostoma lucius consumed primarily Chirostoma juveniles, cladocerans and copepods. However, results revealed competition reduction within zooplanktivores by niche partitioning: C. consocium for copepods, C. jordani for Bosmina and Diaphanosoma and C. labarcae for Daphnia and Ceriodaphnia. Third, we analyzed the water-level fluctuation influence on two niche dimensions of the zooplanktivorous guild. Distribution patterns were determined at two temporal scales: seasonal (dry and rainy) and interannual (shallow and recovery conditions). Seasonally, segregation was more related to species dominance in the dry season and exclusively related to environmental characteristics in the rainy season. Interannually, contrasting conditions influenced fish structure significantly, and environmental characteristics were emphasized when the lake reached 25% of its volume. A significant difference was detected in the trophic analysis when comparing years of contrasting conditions. In shallow conditions, narrow niche breadth values and high diet overlap indicated interspecific exploitative interaction. In recovered conditions, wide niche breadth values and low niche overlap indicated low species interaction. Fourth, the study of the factors that influence the persistence of the species in a disturbance process were evaluated from a historical analysis of the biotic integrity (IBI). Lake Chapala depth and volume has fluctuated due to combined influences of climate and human activities. Although the fish community has endured previous volume fluctuations, the fisheries and IBI negative trends reflect a recent deterioration process. Persistence of the species results from a combined effect of limnetic distribution, species interactions and fisheries characteristics. Different management strategies must be implemented at contrasting lake conditions, well-defined by a volume threshold, and conservation initiatives related to the placement of protected areas must be enforced.