Juvenile pelagic fishes are integral members of many coastal river communities. Many of these systems are boldly influenced by variable wind stress and freshwater inputs that can increase heterogeneity in estuarine habitat for fishes. We use mobile sonar surveys within the Neuse River Estuary System, NC, USA to assess the distribution and behavioral patterns of juvenile anchovies, Anchoa spp. 25-65 mm TL, over a broad range of spatial scales in relation to diel and seasonal changes in water quality including stratification, hypoxic events and copepod distribution. Results from our study indicate that episodic stratification-induced hypoxic events can reduce suitable habitat volume for anchovies by more than 50%. Furthermore, our sampling suggests that hypoxia causes spatial separation between plankton and the grazing fishes. Under stratified oxygen conditions, we observe higher densities of copepods in hypoxic bottom water. Finally, we report that reductions in available habitat caused an increase in local densities of fishes and may result in increased competition for resources. These spatially explicit data are critical for developing trophic dynamic models that predict the response of fish communities to natural and anthropogenic impacts on the system.