Microfossil (benthic foraminifera) data from coastal areas were collected from state and federally managed lands within the Grand Bay National Estuarine Research Reserve and Grand Bay National Wildlife Refuge, Grand Bay, Mississippi/Alabama; federally managed lands of Bon Secour National Wildlife Refuge on Cedar Island and Little Dauphin Island, Alabama; and municipally managed land around Dauphin Island, Alabama. Samples were analyzed and quantified for foraminiferal census in order to document changes to the coastal wetlands, estuarine environments, and to aid in paleoenvironmental reconstruction. These data provide a baseline dataset for use in future wetland change descriptive and predictive studies and assessments. 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 (https://coastal.er.usgs.gov/ssiees), Barrier Island Evolution Research (BIER) project (https://coastal.er.usgs.gov/bier), and National Fish and Wildlife Foundation-funded Alabama Barrier Island Restoration Feasibility Study (a collaborative study between the U.S. Army Corp of Engineers, Mobile District; the State of Alabama; and the USGS [https://www.usgs.gov/centers/spcmsc/science/alabama-barrier-island-restoration-study]). These projects aim to assess ecological and societal vulnerability that results from long- and short-term physical changes to barrier islands and coastal wetlands. Two sampling surveys were conducted between 2014 and 2015: 14CCT01 (15–19 September 2014; 2014-323-FA), and 15BIM09 (18–20 August 2015; 2015-322-FA). During those two trips, seven Russian peat auger cores were taken from marsh locations. Three cores from Dauphin Island were subsampled and stained with rose Bengal (rB) in the field to indicate life. Four further cores from Dauphin Island and Grand Bay were not stained. At the St. Petersburg Coastal and Marine Science Center all cores were subsampled resulting in a total of 74 subsamples. Samples were processed in the laboratory to four size fractions (63–125 μm, 125–250 μm, 250–850 μm, and >850 μm), of which the 125–250 μm and 250–850 μm fractions were picked at equal proportions of total sample and reported combined (125–850 μm). For additional information regarding foraminiferal collection and/or processing methods, refer to Ellis and others (2017). Further data collected on and surrounding Dauphin Island is presented in Ellis and others (2017) and Ellis and others (2018).