Biological retention of nutrients and other elements in stream ecosystems is ultimately related to the metabolic processes of organisms. Hydrologic interactions between surface water and groundwater in the hyporheic zone can influence metabolism and nutrient retention in aquatic ecosystems. This research addressed several questions concerning metabolism and nitrate-nitrogen (NO3-N) retention in four headwater streams: 1) How do differences in surface-subsurface exchange influence stream ecosystem metabolism and the contribution of the hyporheic zone to ecosystem respiration (R)? 2) How does stream ecosystem NO3-N retention relate to metabolism? 3) What is the contribution of hyporheic zones to ecosystem NO3-N retention?

Reach-level hyporheic R was measured as the difference between whole-stream and benthic R in two streams with differing extent of surface-subsurface exchange, Rio Calaveras and Gallina Creek, NM, USA. Cross sectional area of the hyporheic zone (AH) was estimated using independent measures of hyporheic sediment R. Cross sectional area of the transient storage zone (As) was determined using solute transport modeling. Hyporheic R contributed between 40 and 93% of whole-stream R in the four study reaches, and both the percent contribution and magnitude of R increased as As increased.

The relationship between ecosystem metabolism and NO3-N retention was investigated for the two NM streams, as well as the East Fork of Walker Branch, TN, and Hugh White Creek, NC, USA. Measures of whole-stream metabolism were coupled with measures of NO3-N retention conducted during both day and night. Daytime NO3-N retention was greater than nighttime values for three measures of retention at three sites, and photoautotrophs contribute substantially to NO3-N retention at all four sites.

Retention of NO3-N retention in the hyporheic zone was calculated as the difference between whole-stream and benthic chamber measures of NO3-N uptake. Benthic sediments from the NM streams generally consumed NO3-N whereas benthic sediments from the TN and NC sites generated NO3-N. Hyporheic uptake of NO3-N per unit area of streambed was similar in magnitude or exceeded benthic uptake at three of the sites, while hyporheic uptake was negative at one NM site, suggesting generation of NO3-N.

Stream ecosystem NO3-N retention is linked to ecosystem metabolism. Spatial resolution of these processes suggests that hyporheic zone contributions to both metabolism and NO3-N retention are substantial. Hydrologic interactions between surface waters and ground waters are crucial to nutrient and carbon cycling in stream ecosystems, and these interactions need to be considered when studying the biogeochemistry of streams.