The Cujupe Formation (Upper Cretaceous-?Lower Tertiary) represents the uppermost part of the Itapecuru Group in the eastern margin of the Sao Luis Basin (northern Brazil). This unit consists of deposits formed mainly by tidal processes, and is attributed to tidal channel, subtidal bay fill, tidal shoal/sand flat, and tidal delta depositional settings. Five stratigraphic intervals (US1-US5), defined by discontinuity surfaces (L1-L5) capped by lags, were recognized within this unit. The Cujupe Formation represents the estuarine fill of an incised paleovalley. The estuarine nature of these deposits is suggested by several indirect lines of evidence, including: (1) tidally influenced facies associations that change rapidly over short distances; (2) dominance of tidal-channel deposits; and (3) an ichnological assemblage suggestive of highly stressed, brackish-water conditions. The five units and the bounding surfaces of the Cujupe Formation indicate a complex estuarine setting. Analysis of facies architecture within the stratigraphic intervals points to deposition in an estuary that changed dramatically from a wave-dominated (US1/US2) to a tide-dominated one (US3). Such a change in style records amplification of the tidal prism, which caused flooding of the estuary as the paleocoast dynamics shifted from wave-dominated to tide-dominated conditions. The flooding process is interpreted to reflect rise in relative sea level during the transgression of the paleovalley. The subsequent units (US4 and US5) formed in a tide-dominated estuarine setting, but with increased fluvial influence. Their origin is attributed to high-frequency episodes of progradation that took place during the turnaround from the transgressive to the highstand stage of the estuary evolution.