The southern Bouse Formation (late Miocene–early Pliocene) in Blythe basin, CA-AZ, contains a controversial record of the events that preceded the integration of the developing Colorado River with the Gulf of California. High resolution microfaunal and stable isotope (δ¹⁸O, δ¹³C; VPDB) data from a key outcrop of marl and claystone record an abrupt change in water chemistry that we interpret to be the result of a catastrophic sill breach. Basal marl contains a mix of brackish-water ostracodes and marine foraminifers. Ostracode δ¹⁸O values are slightly negative and 6‰ higher than the host sediment carbonate precipitated in the upper water column, indicating isotopically stratified hydrologic conditions during deposition. Freshwater ostracodes abruptly appear in the overlying sediments in association with marine foraminifers, in conjunction with an abrupt change in the isotopic composition of ostracode and host sediment carbonate. The δ¹⁸O values from brackish and freshwater ostracodes and the host sediment carbonate are similar (~ −10‰), indicating an isotopically well-mixed water body during deposition. Sediment δ¹³C values decrease by 4.5‰ across this transition but ostracode δ¹³C values remain unchanged. We infer that the transition from stratified to well-mixed conditions likely took less than 300 years. The abruptness of this transition is best explained by catastrophic failure of a paleodam that rapidly altered the isotopic composition and salinity of a lake in Blythe basin. A marine or estuarine environment is unlikely. Our interpretation is consistent with other evidence for catastrophic breaching of another lacustrine Bouse Formation-bearing basin to the north.