Amazonian floodplain lakes, distinguished by their water types, are crucial ecosystems for fish biodiversity. In these ecosystems, the annual hydrological cycle, known as the "flood pulse," is the primary driving force for fish productivity, providing habitat and feeding opportunities. However, how seasonal water level changes affect fish assemblages and feeding guild responses in floodplains with varying watershed characteristics is still poorly understood. We conducted a comparative stable isotope study in both a white-water and a black-water floodplain lake to investigate fish trophic dynamics during periods of rising and low water levels. Analyses of a broad taxonomic range of fish (seven orders and 27 families, with 73 and 82 taxa in the studied lakes, respectively) revealed that the fish assemblages in the studied white-water and black-water lakes exhibited different trophic dynamics in response to changes induced by the hydrological cycle. In contrast to the white-water lake, a strong, trophic guild-related effect shaped the delta 13C and delta 15N dynamics in the black-water lake. As a result, the fish assemblage in the black-water lake experienced significant trophic shifts with generally opposite dynamics over the water levels compared to the white-water lake. In the black-water lake, water level changes caused alterations in trophic niche width in almost all analyzed guilds (carnivorous, detritivorous, herbivorous, invertivorous, omnivorous, planktivorous), while this was less consistent in the white-water lake. Our results suggest that the fish assemblage in the nutrient-poor black-water lake is more dependent on the annual flood pulse and associated resources than in the white-water lake. These findings may further imply a relatively higher vulnerability of the black-water lake to alterations in the regular flood pulse compared to the white-water lake, indicating greater stability in feeding conditions and fish trophic dynamics in the latter.