Alaska, U.S.A, is one of the few remaining locations in the world that has fjords that contain temperate tidewater glaciers. Studying such estuarine systems provides vital information on how deglaciation affects oceanographic conditions of fjords and surrounding coastal waters. The oceanographic system of Glacier Bay, Alaska, is of particular interest due to the rapid deglaciation of the Bay and the resulting changes in the estuarine environment, the relatively high concentrations of marine mammals, seabirds, fishes, and invertebrates, and the Bay's status as a national park, where commercial fisheries are being phased out. We describe the first comprehensive broad-scale analysis of physical and biological oceanographic conditions within Glacier Bay based on CTD measurements at 24 stations from 1993 to 2002. Seasonal patterns of near-surface salinity, temperature, stratification, turbidity, and euphoric depth suggest that freshwater input was highest in summer, emphasizing the critical role of glacier and snowmelt to this system. Strong and persistent stratification of surface waters driven by freshwater input occurred from spring through fall. After accounting for seasonal and spatial variation, several of the external physical factors (i.e., air temperature, precipitation, day length) explained a large amount of variation in the physical properties of the surface waters. Spatial patterns of phytoplankton biomass varied throughout the year and were related to stratification levels, euphoric depth, and day length. We observed hydrographic patterns indicative of strong competing forces influencing water column stabillity within Glacier Bay: high levels of freshwater discharge promoted stratification in the upper fjord, while strong tidal currents over the Bay's shallow entrance sill enhanced vertical mixing. Where these two processes met in the central deep basins there were optimal conditions of intermediate stratification, higher light levels, and potential nutrient renewal. These conditions were associated with high and sustained chlorophyll a levels observed from spring through fall in these zones of the Bay and provide a framework for under-standing the abundance patterns of higher trophic levels within this estuarine system.