An exhumed Pliocene estuarine sequence is preserved in exquisite detail in the Quinault Formation of coastal western Washington. The thick fill of the Quinault estuarine basin (∼700 m) represents a single transgressive-regressive system that was punctuated by subduction-related tectonic events, and may reflect erosion and sediment accumulation during accelerated uplift of the Olympic Mountains in the Pliocene. Sedimentation patterns in the ancient Quinault estuary were influenced strongly both by floods on the paleo-Quinault River, and by storm waves on the high-energy, open Pacific coast. Body fossils were derived from both marine and brackish faunal elements. Trace fossil suites indicate that the benthos flourished in the fluctuating physicochemical conditions of an estuary in dynamic equilibrium. An estuarine-specific trace fossil, a new ichnospecies of Psilonichnus that is attributed to burrows of the mud shrimp Upogebia pugettensis, is restricted to inlet-mouth, muddy sandstone facies. The marine-marginal marine transition is well-preserved in Quinault estuarine strata (exposed in the Point Grenville and Cape Elizabeth areas), as evidenced by: (1) distinctive sedimentologic signatures characteristic of lower shoreface, estuarine mouth, central basin, tidal creek/flat, and fluvial subenvironments; and, (2) systematic changes in trace fossil associations in the up-estuary direction, from Skolithos ichnofacies elements to a mixed Skolithos-Cruziana assemblage to Glossifungites associations with rhizome phytoburbation. Hence, Quinault strata record a classic tripartite division of an ancient estuarine system, allowing a fine-scale delineation of subenvironments in an active tectonic regime.