Increased water clarity associated with zebra mussel (Dreissena polymorpha) populations may favor benthic algal primary production in freshwater systems previously dominated by pelagic phytoplankton production. While zebra mussel-mediated water clarity effects on benthic primary production have been implicated in published reports, few production estimates are available. This study estimates benthic primary production in Oneida Lake, NY before and after zebra mussel invasion (1992), using measured photosynthetic parameters (, alpha(B) and beta) from sampled benthic algal communities. In the summers of 2003 and 2004, primary production was measured as O(2) evolution from algal communities on hard (cobble) and soft (sediment) substrate from several depths. We also backcast estimates of benthic primary production from measurements of light penetration since 1975. Estimates of whole-lake epipelic and epilithic algal primary production showed a significant (4%) increase and exhibited significantly less interannual variability subsequent to the establishment of zebra mussels. We applied our model to two lakes of differing trophic status; the model significantly overestimated benthic primary production in a hypereutrophic lake, but there was no significant difference between the actual and predicted primary production values in the oligotrophic lake. The hypereutrophic lake had higher zebra mussel densities than Oneida (224 vs. 41 per sample respectively). Though total community respiration (measured in total darkness) was factored into our model predictions of production, our model may need modification when heterotrophic respiration is a large portion of total community metabolism.