Studies of foraminiferal assemblages in intertidal marshes and subtidal creeks usually rely upon sediment samples collected along transects, such that associations with other organisms often go unnoticed. We show that ecologically useful data can be obtained by sampling that is stratified by substrate and microenvironment. The tidal wetland at Lower LaHave, Nova Scotia, Atlantic Canada (44º16′37.39″N, 64º19′46.45″W, area ∼1 km2) comprises mostly sandy sediment occupied largely by the low marsh grass Spartina alterniflora. The wetland is situated next to LaHave Estuary, which is polluted with domestic waste. Microenvironments within the marsh were sampled for total (living + dead) foraminiferal assemblages. The mass of dried sediment examined at each site was used to calculate the foraminiferal number (FN, number of foraminiferal tests per gram of sediment). Sediment samples from the intertidal grass beds reflect a typical low- to high-marsh zonal distribution of benthic foraminifera [FN = 24.7 ± 16.6 g−1 (mean ± standard deviation); n = 716 tests]. Samples from a tidal channel yielded few tests (FN = ∼0.3 ± 0.7 g−1; n = 22). Clutches of the mussel Mytilus edulis occurred in areas of strong current action within the channel and on lower energy slip-off slopes. Mussel clutches from the channel base yielded few tests (FN = ∼0.7 ± 0.7 g−1; n = 25), mostly Miliammina fusca. Clutches from slip-off slopes yielded a significantly richer assemblage (FN = 8.7 ± 4.6 g−1; n = 229) dominated by Elphidium umbilicatulum. We concluded that mussel clutches in low energy areas can be suitable habitat for E. umbilicatulum, either associated with structural complexity of the clutches or with waste products excreted by mussels that may stimulate growth of bacteria or microalgae upon which the foraminifera feed. The results from this study provide a baseline for examining the biotic impact of remediation of the LaHave River on the Lower LaHave wetland.