A three-dimensional computer model of canopies of the seagrass Amphibolis griffithii was used to investigate the consequences of variations in canopy structure and benthic light environment on leaf-level photosynthetic saturation state. The model was constructed using empirical data of plant morphometrics from a previously conducted shading experiment and validated well to in-situ data on light attenuation in canopies of different densities. Using published values of the leaf-level saturating irradiance for photosynthesis, results show that the interaction of canopy density and canopy-scale photosynthetic response is complex and non-linear, due to the combination of self-shading and the non-linearity of photosynthesis versus irradiance (P-I) curves near saturating irradiance. Therefore studies of light limitation in seagrasses should consider variation in canopy structure and density. Based on empirical work, we propose a number of possible measures for canopy scale photosynthetic response that can be plotted to yield isoclines in the space of canopy density and light environment. These plots can be used to interpret the significance of canopy changes induced as a response to decreases in the benthic light environment: in some cases canopy thinning can lead to an equivalent leaf level light environment, in others physiological changes may also be required but these alone may be inadequate for canopy survival. By providing insight to these processes the methods developed here could be a valuable management tool for seagrass conservation during dredging or other coastal developments.