We used whole-stream and benthic chamber methods to measure rates of metabolism and determine the contribution of the hyporheic zone to ecosystem respiration (R) in two streams with differing surface-subsurface exchange characteristics, Rio Calaveras and Gallina Creek, New Mexico. We used the difference between whole-stream and benthic R to calculate the rate of hyporheic zone R and coupled this estimate to an independent measure of hyporheic sediment R to estimate the cross-sectional area of the hyporheic zone (AH) for two reaches from each stream. Conservative tracer injections and solute transport modeling were used to characterize surface-subsurface hydrologic exchange by determining values of the cross-sectional area of the transient storage zone (As). The hyporheic zone contributed a substantial proportion of whole-stream R in all four study reaches, ranging from 40 to 93%. Wholestream R, hyporheic R, and percent contribution of hyporheic R all increased as transient storage increased, with whole-stream and hyporheic R exhibiting significant relationships with As. All three measures of respiration and values of AH were much greater for both reaches of the stream with greater surface-subsurface exchange. AH is valuable for cross-site comparisons because it accounts for differences in rates of both benthic and hyporheic sediment R and can be used to predict the importance of the hyporheic zone to other stream ecosystem processes.