The dominance of warm saline bottom water during the mid-Cretaceous and the early Cenozoic has been inferred from sea-floor sediment records, an interpretation supported by early ocean general circulation model experiments. Thermohaline circulation depends in part on upper ocean salinities; however, early ocean models neglected continental runoff, a potentially critical factor in the salinity budget of the surface ocean. Our early Eocene ocean model sensitivity tests show that model deep-water sources can be enhanced, diminished, or turned off by varying the treatment of continental runoff in the atmosphere-ocean moisture flux calculation. Failure to treat surface runoff adequately thus has important implications for the simulation of thermohaline flow and formation of warm saline bottom water. Variations in runoff could have led to rapid changes in the relative importance of high-latitude versus subtropical deep water, such as may have occurred during the late Paleocene–early Eocene boundary interval (≈ 53.6–56.2 Ma).