The recent 2000-2001 drought resulted in substantially reduced river flows that, in turn, markedly affected water properties, as shown by data collected by Washington State’s Puget Sound Ambient Monitoring Program and the Joint Effort to Monitor the Strait. A ‘densification’ was apparent in the waters throughout Puget Sound, as indicated by a reduction in the density difference between the surface and bottom of the water column. The reduction in the stratification was due to higher salinity surface waters. This observation is notable because stratification regulates numerous biological and physical processes, including the timing of the spring phytoplankton blooms, mixing and flushing. Furthermore, we observed that changes in the density gradient in the Strait of Juan de Fuca led to a marked reduction in the geostrophic exchange velocity (linked to flushing) during the drought year as compared with the higher flow year of 2001-2002. This difference has implications for larval and plankton dispersal/retention and water quality.