The determination of the primary factors controlling carbon (C) transfer rates in situ are a basic requirement for developing a mechanistic view of the processes that regulate benthic microbial community structure and function. In many estuarine ecosystems, the base of the food web is dominated by microalgal production; however, information on the quantitative relationships and process rates of meiofaunal grazers and benthic microalgal (BMA) producers is limited to a few habitats and short temporal scales. The primary objective of this study was to examine the trophic interactions between meiofaunal grazers and BMA producers to determine if grazing is a primary limiting factor for BMA biomass and productivity in Terrebone Bay, Louisiana. Sediment cores were collected from 24 intertidal locations in June 1999 and January 2000 to quantify meiofaunal abundance and grazing rates as well as BMA biomass, community composition and productivity. In June, the benthic community was characterized by high meiofaunal abundances, while BMA showed lower biomass and a shift in community composition towards increased cyanobacteria relative abundance. Measurements in January showed lower meiofaunal abundances, but high BMA biomass dominated by diatoms. However, BMA primary productivity was the same for both sampling dates. Statistical tests revealed a significant interaction between sampling date and meiofauna grazing responses and suggests that the trophic relationships were different in January and June. Meiofaunal grazing, as a percentage of BMA biomass, was high in June (116.7%) and exceeded the available BMA standing stock. However, in both June and January, grazing was less than 16% of the rate of BMA net primary production. During periods of high grazing pressure, BMA community production was more than sufficient to supply food resources for meiofaunal consumers. Our results highlight the tight coupling between microalgae and meiofauna in the upper few millimeters of estuarine sediments. The trophic relationships are complex, with linked feedback mechanisms that operate over small spatio-temporal scales. The coupling of measurements of rate and biomass responses for both producers and grazers provides useful insights into the mechanisms underlying meiofaunal-microalgal trophodynamics.