We examined the effects of a hydrologically restrictive transportation corridor on the nursery use of various habitats in the Mobile-Tensaw River delta (MTD). We compared nekton assemblage structure in fall 2009 and spring 2010 among 3 locations and 3 major habitat types (marsh, submerged aquatic vegetation SAV dominated by Vallisneria americana, and shallow non-vegetated bottom SNB) commonly found throughout the MTD using 1 m2 drop samplers. Sample locations (Tensaw River: TR, Chocolatta Bay: CB, and Below Causeway: BC) were selected based on their degree of tidal connectivity with the wider estuary (TR CB BC). Nekton assemblages varied among locations and habitat types. Recruitment by the young of transient fishery species appeared to drive the nekton assemblage structure at the least hydrologically restricted locations (BC and TR) in the delta, whereas estuarine-resident species dominated the nekton assemblage at CB. Species richness was greater at BC than at CB. Within locations, mean densities of abundant species were concentrated in SAV and marsh. Delta locations directly connected to Mobile Bay, therefore, likely provide an important nursery for fishery species such as white shrimp, blue crab, gulf menhaden, and southern flounder. Additional studies will be needed, however, to determine whether these fishery species represent strong conduits for cross ecosystem transfer of energy and nutrients between the delta and northern Gulf of Mexico.