Detailed analysis of modern and Pleistocene deposits at Willapa Bay, Washington concentrated on identifying ichnological and sedimentological characteristics of five estuarine subenvironments. These include: (1) intertidal flat deposits, which are typically thoroughly bioturbated by a somewhat diminutive suite of various vertical and horizontal shafts and burrows that are locally cross-cut by robust crustacean dwellings; (2) unburrowed to rarely burrowed tidal creek point-bar deposits, which are sporadically burrowed by minute Gyrolithes, Skolithos, Cylindrichnus, Planolites, Palaeophycus, and rare bivalve equilibrichnia; (3) fluvially-through tidally-influenced main point-bar deposits, which are sporadically bioturbated with vertical traces superimposed upon inclined heterolithic stratification; (4) well to thoroughly bioturbated bay deposits, burrowed by relatively robust forms of Ophiomorpha, Teichichnus, Skolithos and bivalve equilibrichnia; and (5) locally bioturbated channel-bar deposits, typically displaying robust bivalve equilibrichnia, rare Ophiomorpha, and deep-penetrating Skolithos. Traces from both the modern and ancient deposits display a marked reduction in size and diversity in the upper estuary. Ongoing research at Willapa Bay confirms the validity of the brackish-water model and provides data that potentially improve our understanding of these deposits. Our findings suggest that strong textural controls are overprinted by salinity stresses; commonly vertical deposit-feeding structures, made by infauna that are mining and/or stoping organic-rich laminae, are present; and there is a potential for the presence of large diameter crustacean burrows in brackish deposits. This research emphasizes ichnologic variability due to autocyclic changes and climatic variability, and urges caution when integrating ichnologic and sedimentologic data into a genetic stratigraphic model.