Across the 20th century, Puerto Rico faced significant development of freshwater systems through channelization, embankment, and dam projects. The damming of rivers create a novel environment that affects river continuity and the affinity of species to aquatic environments above, in, and below the dam. This study focuses on the influence of reservoir structure on species abundance, growth, and trophic interactions within the Curias Reservoir and Isabella Retention Pond, a spillway-embankment and a retention pond, respectively. The reservoirs differ in use, structure, age, and connection to freshwater ecosystems. The methods consist of long-term censuses conducted across each reservoir: the littoral zone, the transitional zone, the inlet, and the outlet. The captured fish and decapods were measured, weighed, photographed, and dissected to quantify stomach contents. Both reservoirs were dominated by introduced cichlid species and other large-bodied, low-trophic-level fish, such as tilapiine cichlids, midas cichlids, and armored catfish. The Curias Reservoir has a greater diversity of fish and decapods, and it supports native shrimp species. The species assemblage within the Isabella Retention Pond was dominated by non-native fish and decapod species, including the Australian redclaw crayfish. The Curias Reservoir connection to the main river channel, the natural littoral zones (vegetation and sediment), and a funnel-shaped spillway structure allow colonization by native decapod species. The fish show intra- and interspecific variation in weight, length, and shape, including snout projection and body depth, between both locations. The fish from the Curias Reservoir had significantly greater weights at equal lengths than those in Isabella Retention Pond. River embankment cichlids were more robust, showed slower growth scaling, and had distinctive reproductive traits. Moreover, the fish assemblages within Isabella Retention Pond showed greater constraints on functional diversity and traits than those in the Curias Reservoir. The Curias Reservoir fish stomach contents demonstrated greater niche partitioning and trophic levels, with representation of piscivore, herbivore, and detritivore species; however, both reservoir types were dominated by generalist and benthic foraging species. These results indicate how reservoir structure, stability, and connectivity strongly mediate species colonization, growth, functional diversity, and trophic interactions within fish communities.