Microfossil (benthic foraminifera) and coordinate/elevation data were obtained from sediments collected in the coastal zones of Mississippi and Alabama, including marsh and estuarine environments of eastern Mississippi Sound and Mobile Bay, in order to develop a census for coastal environments and to aid in paleoenvironmental reconstruction. These data provide a baseline dataset for use in future wetland and estuarine change studies and assessments, both descriptive and predictive types. 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. Four sampling surveys were conducted between 2013 and 2016: 13BIM01 (14–18 April 2013; no FA numbering), 14CCT01 (15–19 September 2014; 2014-323-FA), 15BIM09 (18–20 August 2015; 2015-322-FA), and 16CCT03 (16–17 May 2016; 2016-331-FA). During the four trips, 168 replicate sedimentary samples were collected from 86 marsh and estuarine locations. The sediment samples were collected from various coastal environments, stained in the field with rose Bengal (rB) to indicate life, 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). Foraminifera were identified to species level under a binocular microscope and counted to establish a census. For further information regarding foraminiferal collection and/or processing methods, refer to Ellis and others (2017). For related datasets from the Mississippi Sound area, please refer to Ellis and others (2017) and DeWitt and others (2017).