The "fundamental niche" is the range of conditions under which an organism can survive and reproduce, measured in the absence of biotic interactions. Niche measurements are often based on statistical relationships between species presence and measured environmental variables, or inferred from measured responses of species along hypothesized niche axes. In this study, we use novel, process-based models of how irradiance and gas diffusion influence photosynthesis and respiration to predict niche dimensions for three coral species: Acropora nasuta, Montipora foliosa, and Leptoria phrygia. We use a combination of mathematical modeling, laboratory experiments, and field observations to establish the link between energy acquisition and the dominant environmental gradients on reefs: light intensity and water flow velocity. Our approach allows us to quantify how the shape of the niche varies in response to light and flow conditions. The model predicts that, due to its higher photosynthetic capacity, the branching coral A. nasuta has a positive energy balance over awider range of conditions than both a massive species (L. phrygia) and a foliose species (M. foliosa). Moreover, colony size influences niche width, with larger colonies of all three species achieving a positive energy balance over a broader range of conditions than small colonies. Comparison of model predictions with field data demonstrated that tissue biomass and reproductive output are significantly and positively correlated with predicted energy acquisition. These results show how interactions between light and flow determine organism performance along environmental gradients on coral reefs. In addition, this study demonstrates the utility of process-based models for quantifying how physiology influences ecology, and for predicting the ecological consequences of varying environmental conditions.