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Metabolism was measured in four Michigan streams, comparing estimates made using a flow-through chamber designed to include the hyporheic zone to a 20 cm depth and a traditional closed chamber that enclosed to a 5 cm depth. Mean levels of gross primary productivity and community respiration were consistently greater in the flow-through chamber than the closed chamber in all streams. Ratios of productivity to respiration (P/R) were consistently greater in the closed chambers than the flow-through chambers. P/R ratios were consistently <1 in all streams when estimated with flow-through chambers, suggesting heterotrophic conditions. Maintenance of stream ecosystem structure and function therefore is dependent on subsidies either from the adjacent terrestrial system or upstream sources. Our results suggest that stream metabolism studies that rely on extrapolation of closed chambers to the whole reach will most likely underestimate gross primary productivity and community respiration.