The Paranagua Bay estuary is a 50 km long microtidal barrier estuary that is still far from infilled even after 3.5 m of continuous sea-level fall during the last 5000 years. Data derived from several independent studies, including surface sediment samples, jet-probe cores, vibracores, and seismic records, were compiled in order to provide an assessment of the Quaternary stratigraphy of the estuary. The estuary displays the longitudinal tripartite zonation of surface sedimentary facies (marine sand-estuarine mud-fluvial sand) that is characteristic of many coastal-plain estuaries. Five sedimentary facies were identified overlying the bedrock. Pre-Holocene fluvial and continental deposits within the paleovalley form the substrate for the more recent sedimentation. A transgressive mud facies marks the initial stages of estuary inundation. This deposit is observed only in the lower half of the estuary, where greater accommodation space existed and less intensive tidal scouring associated with the subsequent deposition of the transgressive sand facies occurred. The onset of the regressive stage is marked by the deposition of the regressive mud facies, which is presently the most extensive sedimentary deposit within the estuary. The regressive sand facies, which is composed of fluvially derived sediments and is restricted to the head of the estuary, is the least developed sedimentary facies. The vertical succession of the sedimentary facies shows an almost complete stratigraphic sequence and the presence of several bounding surfaces: a transgressive surface, a maximum flooding surface, a tidal ravinement surface, and a tidal diastem. A comparison of the Paranagua Bay, Gironde, and James estuaries, all of similar size, illustrates various stages of sequence development in modern incised-valley systems.