Little is known about the relative contribution of different stream habitats to reach-scale metabolism. We measured in situ metabolism in sand, gravel, stone, and macrophyte habitats to compare metabolic rates among these habitat types and to compare habitat-weighted measurements with reach-scale measurements. We used open-bottom chambers in sand, gravel, and macrophyte habitats and closed-bottom chambers in stones, and we estimated reach-scale metabolism from 2-station O2 budgets. Macrophyte habitats had a significantly higher gross primary production (GPP) and community respiration (CR) than stone, gravel, and sand habitats. A large part of this difference was associated with epiphytic biofilm: 28% of net ecosystem production (NEP), 20% of CR, and 24% of GPP. Macrophyte habitats contributed proportionally more to reach-scale metabolism than did the other habitat types. Forty-one percent of reach-scale NEP, 60% of ecosystem respiration (ER), and 50% of GPP were associated with this habitat type even though only 14% of the reach was covered by macro-phytes. We found significant linear relationships between GPP and CR and the amount of autotrophic biomass in the streams. The rates reported in 11 literature studies fit into our observed relationships, showing the generality of our findings. The rates we obtained expand the range of reported metabolic values in relation to auto-trophic biomass for both low and high biomass. The importance of macrophyte habitat can be ascribed to the macrophytes themselves, the associated epiphytic biofilm, and the fine organic material trapped in the dense stands. We conclude that besides having an effect on the structural elements in streams, macrophytes contribute significantly to stream ecosystem functions.