We used whole-stream and benthic chamber methods to measure rates of metabo
lism and determine the contribution of the hyporheic zone to ecosystem resp
iration (R) in two streams with differing surface-subsurface exchange chara
cteristics, Rio Calaveras and Gallina Creek, New Mexico. We used the differ
ence between whole-stream and benthic R to calculate the rate of hyporheic
zone R and coupled this estimate to an independent measure of hyporheic sed
iment R to estimate the cross-sectional area of the hyporheic zone (A(H)) f
or 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 (A(s)). The hyporheic zone contributed a substantial proporti
on of whole-stream R in all four study reaches, ranging from 40 to 93%. Who
le stream R, hyporheic R, and percent contribution of hyporheic R all incre
ased as transient storage increased, with whole-stream and hyporheic R exhi
biting significant relationships with A(s). All three measures of respirati
on and values of A(H) were much greater for both reaches of the stream with
greater surface-subsurface exchange. A(H) is valuable for cross-site compa
risons because it accounts for differences in rates of both benthic and hyp
orheic sediment R and can be used to predict the importance of the hyporhei
c zone to other stream ecosystem processes.