This study examined the contribution of benthic microalgae to total microalgal production in the Weeks Bay National Estuarine Research Reserve, a shallow subtidal estuarine ecosystem in Baldwin County, Alabama, USA. Environmental characteristics, nutrient concentrations, and benthic and planktonic biomass and productivity rates were measured every 2-4 weeks between February 1991 and August 1992. Chlorophyll-a concentrations in the surficial sediments ranged from 0.2 to 30.7 mg m(-2), with a mean of 9.5 +/- 1.5 mg m(-2) for the study period. Over an annual cycle, benthic microalgae contributed 25.2% of total microalgal biomass. Daily production rates for the benthic microalgae ranged from 0.01 to 0.75 gC m(-2) d(-1), with a mean of 0.22 +/- 0.05 gC m(-2) d(-1). Annual production of the benthic microalgae was 90.1 gC m(-2), or 20.6% of total microalgal production in Weeks Bay. Stepwise multiple regression revealed that nitrate, planktonic chi-a, benthic production, and seston accounted for 33% of the variability in benthic microalgal biomass, while light, seston, nitrate and benthic chi-a accounted for 36% of the variability in benthic microalgal production. This study suggests that, in this environment, the relative importance of benthic microalgal production is not regulated by any single factor, but rather is highly variable as a result of physical mixing and resuspension processes.