Abstract Hydrography and tidal circulation are described for two deep fjords (Whale Bay and Eaglek Bay) and two shallow bays (Simpson Bay and Zaikof Bay) used as nursery habitat by juvenile Pacific herring (Clupea pallasi) in Prince William Sound, Alaska from October 1995 to March 1998. The seasonal hydrography varied markedly among the four locations due to the interaction of various factors including local climate, hydrology, advection of allochthonous glacial water, and vertical mixing from winds and tides. The fjords exhibited strong haline stratification in the summer that persisted into winter. In contrast, the bays exhibited brief periods of weak to strong stratification that dissipated early in the autumn. The timing of peak freshwater input also varied among locations depending on the maximum size and elevations of watersheds and the extent of precipitation stored within alpine snow and ice fields. In late winter (March), surface water in the fjords was relatively cold (1–3 °C) and slightly fresh (29–30 psu) in comparison to the bays (3.5–5.5 °C and 31–31.5 psu). The subsurface water (40–80 m) was warmer in the fjords (5–7 °C), whereas the bays exhibited vertically uniform temperature and salinity (T/S) properties. Tidal currents were typically highest near the mouth of most basins (35–150 cm s−1) and exhibited horizontal and vertical shear in the summer and autumn. During these seasons, these flows created baroclinic currents within most basins, anticyclonic eddies at Simpson and Zaikof bays, and inflow of allochthonous glacial water at Whale Bay. Local climate and watershed hydrology of individual bays have a strong influence on water temperatures and haline stratification, which potentially affect production of phytoplankton, zooplankton, and growth and survival of age-0 herring. Additionally, variability in transport of Gulf of Alaska derived carbon sources into nursery bays is dependent on geographical location and the physical features of each basin, such as maximum depths, presence or absence of sills, and spatial patterns in the winds and currents.