On Conch Reef, Florida Keys, USA we examine the interaction of local hydrography and the complex reef topography on the pattern of stable isotope (δ18O and δ13C) signatures in the benthic green algae, Halimeda tuna.  During the summer months, benthic temperatures show high-frequency fluctuations associated with the arrival of internal waves that advect cool, nutrient rich water across the reef slope. The nutrient and temperature regime available for H. tuna growth across the reef is modified by the interaction between local water flow and reef morphology and results in a highly heterogenous growth environment even within isobaths. This environmental heterogeneity in then reflected in the large variability in isotopic signatures even among closely located individuals. Comparing the temperature measured across the reef front with that predicted by the δ18O isotopic thermometer suggests complex interactions between the environment and Halimeda carbonate formation at temporal and spatial scales not normally considered in mixed or averaged sediment samples. The divergence in estimated temperature range between measured and predicted temperatures emphasizes species and location specific temperature relationships. The relatively light δ18O signatures, compared to other model measurements, may also indicate freshwater input at Conch Reef. These observations illustrate the need to consider this spatial heterogeneity in contemporary as well as ancient reef settings that are influenced by a similar, highly variable physical environment.