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Energy flow and nutrient cycling dictate the functional role of organisms in ecosystems. Fishes are key vectors of carbon (C), nitrogen (N) and phosphorus (P) in aquatic systems, and the quantification of elemental fluxes is often achieved by coupling bioenergetics and stoichiometry. While nutrient limitation has been accounted for in several stoichiometric models, there is no current implementation that permits its incorporation into a bioenergetics approach to predict ingestion rates. This may lead to biased estimates of elemental fluxes. Here, we introduce a theoretical framework that combines stoichiometry and bioenergetics with explicit consideration of elemental limitations. We examine varying elemental limitations across different trophic groups and life stages through a case study of three trophically distinct reef fishes. Further, we empirically validate our model using an independent database of measured excretion rates. Our model adequately predicts elemental fluxes in the examined species and reveals species‐ and size‐specific limitations of C, N and P. In line with theoretical predictions, we demonstrate that the herbivore Zebrasoma scopas is limited by N and P, and all three fish species are limited by P in early life stages. Further, we show that failing to account for nutrient limitation can result in a greater than twofold underestimation of ingestion rates, which leads to severely biased excretion rates. Our model improved predictions of ingestion, excretion and egestion rates across all life stages, especially for fishes with diets low in N and/or P. Due to its broad applicability, its reliance on many parameters that are well‐defined and widely accessible, and its straightforward implementation via the accompanying r ‐package fishflux , our model provides a user‐friendly path towards a better understanding of ecosystem‐wide nutrient cycling in the aquatic biome.