We measured metabolism in mid-channel and river-edge microhabitats in the Susquehanna River of central Pennsylvania during fall 2007 to determine if microhabitat affects susceptibility to eutrophication.  Velocity and depth were >10x higher in mid-channel than along river margins, and water flowing along river margins was effectively isolated from mid-channel water by submerged gravel bars and thick algal mats (especially Cladophora spp.).  Gross primary production (GPP) and respiration (R) were extremely high in river margins (GPP 17.13 mg O₂/L/d, R 17.63 mg O₂/L/d) and were consistently higher than in mid-channel (GPP 5.74 mg O₂/L/d, R 4.45 mg O₂/L/d).  These dramatic differences in metabolism, coupled with physical differences in velocity and depth, resulted in distinct patterns of dissolved oxygen concentration.  Oxygen concentrations fluctuated from 4.13 mg/L (43% saturation) at nighttime to 13.79 mg/L (168% saturation) in mid-afternoon along the river margin.  Mid-channel diel fluctuation in oxygen concentrations was only 9.15-11.18 mg/L and remained relatively close to saturation (93-120%).  Physical characteristics along margins may reduce resistance to eutrophication in shallow rivers and cause poor conditions for aquatic organisms by reducing transport of senescent algae, limiting gas exchange with the atmosphere, and concentrating effects of biological processes on dissolved oxygen concentrations.