Marine straits and seaways are known to host a wide range of sedimentary processes and products, but the role of marine connections in the development of large river systems remains little studied. This study explores a hypothesis that shallow-marine waters flooded the lower Colorado River valley at c. 5 Ma along a fault-controlled former tidal strait, soon after the river was first integrated into the northern Gulf of California. The upper bioclastic member of the southern Bouse Formation provides a critical test of this hypothesis. The upper bioclastic member contains wave ripple-laminated bioclastic grainstone with minor red mudstone, pebbly grainstone with hummocky cross-stratification (HCS)-like stratification and symmetrical gravelly ripples, and calcareous-matrix conglomerate. Fossils include upward-branching segmented coralline-like red algae with no known modern relatives but confirmed as marine calcareous algae, echinoid spines, barnacles, shallow-marine foraminifers, clams, and serpulid worm tubes. These results provide evidence for deposition in a shallow-marine bay or estuary seaward of the transgressive backstepping Colorado River delta. Tsunamis generated by seismic and meteorological sources likely produced the HCS-like and wave-ripple cross-bedding in poorly-sorted gravelly grainstone. Marine waters inundated a former tidal strait within a fault-bounded tectonic lowland that connected the lower Colorado River to the Gulf of California. Delta backstepping and transgression resulted from a decrease in sediment output due to sediment trapping in upstream basins and relative sea-level rise produced by regional tectonic subsidence.