Abstract Foraminiferal assemblages of Bombay Hook National Wildlife Refuge (Smyrna, Delaware, U.S.A.) exhibit substantial variation in spatio-temporal test inputs to marsh sediment and are strongly overprinted by seasonal changes in porewater chemistry. Seasonal surface and near-surface samples are typically not representative of foraminiferal inputs at depth (60 cm). Long-term ecological signals are detected using artificially time-averaged (ATA) assemblages, in which dead and live counts of foraminifera are summed separately for an entire two-year sampling period. Unlike seasonal assemblages, cluster analysis of ATA assemblages reveals a distinct change in assemblages at ∼ 20 cm depth. Differential preservation of foraminifera in the upper 60 cm—and especially the upper 20 cm—of sediment mimics a sharp paleoenvironmental change that could potentially be interpreted as a rapid fall in sea level during a time of documented transgression over the last ∼ 100–200 years.