Microfossil (benthic foraminifera) samples were obtained from surficial grab (denoted with “G”) and push core (denoted with “M”) sediments collected in Grand Bay estuary, Mississippi and Alabama, to aid in the paleoenvironmental understanding of Grand Bay estuary. The data presented here were collected as part of the U.S. Geological Survey’s Sea-level and Storm Impacts on Estuarine Environments and Shorelines (SSIEES) project, and Barrier Island Evolution Research (BIER) project. Sampling was conducted in May 2016 [field activity number (FAN) 2016-331-FA, alternate FAN 16CCT03]. In the field, 15 cores were collected in tidal creek mouths, proximal to tidal creek mouths, in protected coves, and in the open Grand Bay estuary. Surface samples were collected at each core site location. At the St. Petersburg Coastal and Marine Science Center (SPCMSC), 13 of the 15 cores were selectively subsampled for foraminifera, resulting in a total of 64 push core subsamples. Estuarine surface grab samples and push core subsamples were processed in the laboratory to three size fractions (63–125 micrometers (μm), 125–850 μm, and >850 μm), of which the 125–850 μm fraction was picked. The raw foraminiferal count data from the picked subsamples are provided below. For further information regarding foraminiferal collection and/or processing methods, refer to Ellis and others (2017a, https://doi.org/10.3133/ds1060). For information regarding 16CCT03 site locations, water quality parameters and sediment properties, refer to Marot and others (2019, https://doi.org/10.5066/P9FO8R3Y). For related datasets from the Mississippi Sound area, please refer to Haller and others (2018a, https://doi.org/10.5066/F7MC8X5F; and 2018b, https://doi.org/10.5066/F7445KSG), Ellis and others (2018, https://doi.org/10.3133/ofr20171165), Ellis and others (2017b, https://doi.org/10.3133/ds1046), and DeWitt and others (2017, https://doi.org/10.3133/ds1070). Downloadable data are available as Excel spreadsheets, comma-separated values text files, and formal Federal Geographic Data Committee metadata.