Distributed hydraulic and water quality property characterization aides in understanding a broad range of river issues including confluence and discharge mixing phenomena, groundwater-surface water exchanges, and mapping flow and temperature distributions in the context of habitat restoration efforts. In this work, we characterize the Merced-San Joaquin River confluence zone using rapidly deployable networked infomechanical systems (NIMS RD) technology. NIMS RD robotically delivers velocity (ADV) and multi-parameter water quality sensors to points in a river transect. This presentation provides an overview of the NIMS RD equipment, deployment methods, and results from a seven-day period in August, 2007, upstream and downstream transects were obtained describing velocity, temperature, electrical conductivity (EC), pH, dissolved oxygen and oxidation-reduction potential (ORP) at one upstream each for the Merced and San Joaquin Rivers and two transects approximately 100 and 400m downstream of the effluent. Velocity and water quality parameter distributions are presented for transects above and within the mixing zone of the confluence zone using high resolution raster scans. Results are discussed in terms of river mixing processes and flow and solute mass balance calculations aimed at identifying and quantifying groundwater inputs.