We assessed spatial and temporal variability in the physical environment of a subarctic estuary, and examined concurrent patterns of chlorophyll α abundance (fluorescence), and zooplankton and forage fish community structure. Surveys were conducted in lower Cook Inlet, Alaska, during late July and early August from 1997 through 1999. Principle components analysis (PCA) revealed that spatial heterogeneity in the physical oceanographic environment of lower Cook Inlet could be modeled as three marine-estuarine gradients characterized by temperature, salinity, bottom depth, and turbidity. The gradients persisted from 1997 through 1999, and PCA explained 68% to 92% of the variance in physical oceanography for each gradient-year combination. Correlations between chlorophyll α abundance and distribution and the PCA axes were weak. Chlorophyll was reduced by turbidity, and low levels occurred in areas with high levels of suspended sediments. Detrended correspondence analysis (DCA) was used to order the sample sites based on species composition and to order the zooplankton and forage fish taxa based on similarities among sample sites for each gradient-year. Correlations between the structure of the physical environment (PCA axis 1) and zooplankton community structure (DCA axis 1) were strong (r = 0.43-0.86) in all years for the three marine-estuarine gradients, suggesting that zooplankton community composition was structured by the physical environment. The physical environment (PCA) and forage fish community structure (DCA) were weakly correlated in all years along Gradient 2, defined by halocline intensity and surface temperature and salinity, even though these physical variables were more important for defining zooplankton habitats. However, the physical environment (PCA) and forage fish community structure (DCA) were strongly correlated along the primary marine-estuarine gradient (#1) in 1997 (r = 0.87) and 1998 (r = 0.82). The correlation was poor (r = 0.32) in 1999, when fish community structure changed markedly in lower Cook Inlet. Capelin (Mallotus villosus), walleye pollock (Theragra chalcogramma), and arrowtooth flounder (Atheresthes stomias) were caught farther north than in previous years. Waters were significantly colder and more saline in 1999, a La Nina year, than in other years of the study. Interannual fluctuations in environmental conditions in lower Cook Inlet did not have substantial effects on zooplankton community structure, although abundance of individual taxa varied significantly. The abundance and distribution of chlorophyll α, zooplankton and forage fish were affected much more by spatial variability in physical oceanography than by interannual variability. Our examination of physical-biological linkages in lower Cook Inlet supports the concept of "bottom-up control," i.e., that variability in the physical environment structures higher trophic-level communities by influencing their distribution and abundance across space.