Differential gauging and tracer tests resolve seepage fluxes in a strongly-losing stream

Summary The Pajaro River, central coastal California, consistently loses 0.2–0.4 m 3 /s of discharge along an 11.42-km experimental reach late in the water year, when discharge is ⩽4.5 m 3 /s. Channel loss occurs throughout this reach, but is greatest in magnitude near the bottom of the reach. Water isotopic data and other observations suggest that channel loss results mainly from streambed seepage, as opposed to evapotranspiration. If it occurs throughout the year, the channel loss along this short stream reach could contribute 6–13 × 10 6  m 3 of annual aquifer recharge, or ∼20–40% of current sustainable basin yield. We performed a series of tracer injections along this reach to determine if hydrologic exchange occurs within this strongly-losing stream. We found that during periods of high channel loss, there were also comparable storage exchange fluxes and lateral inflow of tracer-free water. Within upper and lower parts of the experimental reach, storage exchange fluxes are about 10 times greater than lateral inflow. The former are associated with the movement of water between the main channel and surface or subsurface storage zones. In this system, it is likely that the latter are primarily associated with spatially- or temporally-long subsurface flow paths within the shallow streambed, as opposed to inflow of ground water from deeper in the basin. Along both upper and lower parts of the experimental reach, lateral inflow tends to increase as channel discharge decreases. In contrast, storage exchange fluxes increase with decreasing discharge along the upper parts of the reach, but decrease with decreasing discharge along the lower parts. Gauging and tracer test results suggest that subsurface storage exchange and loss may occur simultaneously, and that the lateral inflow of tracer-free water can be caused by long-scale subsurface flow as well as ground water making its first appearance in the channel.