Temperate rocky reefs dominated by the giant kelp, Macrocystis pyrifera, support a diverse assemblage of benthic macrophytes that provide vital ecosystem services. This autotrophic community is characterized as having some of the highest rates of primary production in aquatic ecosystems, sequestering atmospheric carbon dioxide and exporting seawater dissolved oxygen (DO) and organic carbon to adjacent ecosystems. Globally, kelp forest ecosystems are facing declines in benthic macrophyte cover, which results in reductions in species diversity and primary productivity. While numerous studies have addressed rates of primary production by kelps and associated understory macrophytes, few have examined how the loss of these species impacts ecosystem functioning on temperate rocky reefs. The goals of this study are to quantify the loss of benthic macroalgae in deforested areas, and to develop a model of kelp forest primary production using associated understory species-specific rates of oxygen evolution paired with field derived productivity estimates. Together, these will elucidate patterns of production, or loss thereof, on reefs dominated by M. pyrifera and adjacent deforested reefs. These measurements were conducted at three locations along the California and Baja California coasts. Algal diversity was lowest but estimates of benthic production were highest in the northernmost site, Stillwater Cove. Algal diversity was highest, but estimates of benthic production were the most variable, in the central site, Point Loma. At the southernmost site, Campo Kennedy, estimates of benthic production were lowest, and benthic production did not scale with diversity. Rather, benthic production was driven by abiotic factors such as available Photosynthetically Active Radiation (PAR). The quantification of species-specific rates of production from benthic macrophytes reveals that assemblage, rather than diversity, is a better predictor of primary reduction on rocky reefs. Interestingly, fluctuations in in situ seawater dissolved oxygen (DO) were not different between reefs where benthic macrophytes were present versus where they were lost. Further, fluctuations in seawater DO did not reveal a biological contribution from benthic macrophytes to productivity, which indicated that, contrary to initial expectations, quantifying in situ DO alone is not sufficient for predicting macrophyte presence or absence or for quantifying primary production on temperate rocky reefs.