The lower Merced River Basin was chosen by the U.S. Geological Survey?s (USGS) National Water Quality Assessment Program (NAWQA) to be included in a national study on how hydrological processes and agricultural practices interact to affect the transport and fate of agricultural chemicals. As part of this effort, surface-water?ground-water (sw?gw) interactions were studied in an instrumented 100-m reach on the lower Merced River. This study focused on estimating vertical rates of exchange across the sediment?water interface by direct measurement using seepage meters and by using temperature as a tracer coupled with numerical modeling. Temperature loggers and pressure transducers were placed in monitoring wells within the streambed and in the river to continuously monitor temperature and hydraulic head every 15 minutes from March 2004 to October 2005. One-dimensional modeling of heat and water flow was used to interpret the temperature and head observations and deduce the sw?gw fluxes using the USGS numerical model, VS2DH, which simulates variably saturated water flow and solves the energy transport equation. Results of the modeling effort indicate that the Merced River at the study reach is generally a slightly gaining stream with small head differences (cm) between the surface water and ground water, with flow reversals occurring during high streamflow events. The average vertical flux across the sediment?water interface was 0.4?2.2 cm/day, and the range of hydraulic conductivities was 1?10 m/day. Seepage meters generally failed to provide accurate data in this high-energy system because of slow seepage rates and a moving streambed resulting in scour or burial of the seepage meters. Estimates of streambed hydraulic conductivity were also made using grain-size analysis and slug tests. Estimated hydraulic conductivity for the upstream transect determined using slug tests ranged from 40 to 250 m/day, whereas the downstream transect ranged from 10 to 100 m/day. The range in variability was a result of position along each transect. A relative percent difference was used to describe the variability in estimates of hydraulic conductivity by grain-size analysis and slug test. Variability in applied methods at the upstream transect ranged from 0 to 9 percent, whereas the downstream transect showed greater variability, with a range of 80 to 133 percent.