We investigated spatial and temporal patterns in macroscopic benthic primary producer biomass, production, and composition in inner Saginaw Bay in 2009 and 2010. Charophytes and filamentous algae (FA) were relatively abundant, and vascular macrophytes were less common. The probability of benthic primary producer presence increased with the proportion of benthic substrate composed of rock. Most benthic primary producer biomass occurred at depths of 2–4 m, with very little biomass observed beyond 4 m deep. Charophyte and vascular macrophyte abundances displayed consistent patterns related to distance from the mouth of the Saginaw River. FA abundance also displayed such patterns, but they reversed between 2009 and 2010. Macrophytic benthic primary producer communities were generally dominated by charophytes. Three genera of vascular macrophytes, including Myriophyllum, were also observed. Filamentous algal communities were composed of a mixture of FA taxa. Ten FA genera were observed, including the red alga Compsopogon. Dominance of Compsopogon was related to low water clarity and low TP. Biomass-based benthic production estimates indicated that charophytes and FA strongly dominated macroscopic benthic production; production of vascular macrophytes was relatively low. The observed relationships of abundance and environmental conditions suggested regulation of benthic producer biomass by a shifting mosaic of substratum, nutrient, and light availabilities. The diverse nature of the benthic producer community could complicate understanding and management of excess benthic biomass and beach fouling in Saginaw Bay.