Streamwater exchange with biogeochemically active hyporheic zones is primarily a function of hydrologic and geomorphic drivers. Thus, there is the potential for strong feedbacks between physical and biogeochemical processes to control nutrient uptake and retention.  To explore the importance of hyporheic nutrient retention to nutrient transport in streams, we measured subsurface biological activity across a watershed area (0.6-145 km²) gradient in six tributaries and the mainstem of the South Fork Eel River in the Coast Range of northern California. The geology and steep slope of the watershed appear to restrict areas of potential subsurface flow compared to gravel and sand bedded rivers. Despite this, rates of microbial activity were relatively high in stream sediments (5.2-17.9 µgO₂*g AFDM^-1*h^-1), as were rates of nutrient uptake (0.5 – 5.9 µg NH₄ / kg sed; 20-50 µg PO₄-P / g sed.). Biotic and abiotic uptake in sediments deeper than 5 cm occurred at rates sufficient to account for a significant proportion of retention of available nutrients transported by streams. In streams which exhibit seasonal patterns in particulate organic matter abundance, the availability of nutrients to benthic food webs could vary temporally as a result of subsurface biology-hydrology feedbacks.