The Pacific Decadal Oscillation (PDO), Multivariate Enso Index and North Pacific Gyre Oscillation (NPGO) all changed signs in 1999, signaling the first shift of the NE Pacific to its cool phase since the 1970's. Regional manifestations of this climate shift included intensification of upwelling, strengthening of southerly flows, cooling of surface waters and increased primary productivity of California coastal waters. Since 1999 we have measured record high abundances of common species of crabs, shrimp and demersal fish and increasing phytoplankton biomass in San Francisco Bay. These regional changes in coastal oceanographic conditions after 1999 promote strong recruitment of marine species that use estuaries as nursery habitat. Annual fluctuations of these populations are strongly correlated with NPGO and PDO which, together, appear to capture dynamics of processes that regulate their annual recruitment. This study, built from three decades of observation, illustrates how regime shifts of the global climate system cascade to the scale of bays and estuaries and can restructure their biological communities. If global warming alters patterns of atmospheric forcing across ocean basins we can, therefore, anticipate responses that will propagate into coastal ecosystems at the land-sea interface. Examples from other estuarine-coastal ecosystems will be used to further illustrate climate-ecosystem linkages.