We gauged and instrumented an 11.42-km long experimental reach of the Pajaro River, central coastal California, to determine rates of streambed seepage (loss and hyporheic exchange) using reach averaged and point specific methods. We used these data to assess changes in streambed hydraulic conductivity with time, as a function of channel discharge and associated changes in sediment scour and deposition. Discharge loss along the experimental reach was generally 0.1-0.3 m(3) s(-1) when channel discharge was <= 2(3) s(-1), with most of the loss occurring along the lower part of the experimental reach. Point specific seepage rates, determined using time-series analysis of streambed thermal records, indicate seepage rates as great as -1.4 m day(-1) (downward into the streambed). Seepage rates varied spatially and with time, with greater seepage occurring along the lower part of the reach and during the summer and fall. Seepage rate and hydraulic gradient data show that streambed hydraulic conductivity was 10(-6)-10(-4) m s(-1) along the experimental reach, with lower conductivity determined later in the dry season, as sediment was deposited on the streambed during low flow conditions. These results suggest that models of surface water-ground water interactions may benefit from inclusion of relations between stream discharge, sediment load, and streambed hydraulic properties. (C) 2010 Elsevier B.V. All rights reserved.