ABSTRACT: Over the past 50 yr, Alaska has warmed at more than twice the rate of the rest of the United States so that climate change impacts are much more pronounced in this region. Simpson and Sheep Bays are pristine fjords in Prince William Sound which differ significantly in terms of size and bathymetry, watershed topography and presence of alpine glaciers. During summers in 2006 to 2008, we investigated the relationship between hydrography and phytoplankton ecology. We found phytoplankton standing stocks and productivity were higher in Simpson relative to Sheep Bay. Phytoplankton physiology (measured with a fluorescence induction and relaxation system) was not significantly different (p > 0.05) in the 2 fjords: F_V/F_M = 0.32 to 0.67, σ_PSII = 141 to 391 Ų quanta^-1, τ_Qa = 125 to 1020 µs, and p = 0.06 to 0.39. Resource (also known as nutrient) limitation assays revealed a gradient of nutrient co-limitation (NSi to NP, respectively) from the delta to the mouth in Simpson Bay. Phytoplankton dynamics were found to be driven by wind mixing and nutrient upwelling which fueled productivity in the upper water column. A comparison of temperature/salinity profiles measured in the present study with those in 1996/1997 revealed a decadal change in hydrography. Both fjords exhibited deep vertical gradients indicative of moderate vertical mixing in 1996/1997, while those measured in 2007/2008 were shallow, with significant stratification. These changes in hydrography, associated with climate change at these high latitudes, will likely lower phytoplankton productivity due to decreased reintroduction of nutrients to surface waters. Consequences to higher trophic levels of reduced food supply require further investigation, including food web and modeling studies.