A temperature TMDL study was completed for MDEQ on the Upper Jefferson River. The Upper Jefferson River is fed from three headwaters and the study length is approximately 41 miles. A water balance and development of rating curves were key aspects to understanding and modeling temperature effects. Temperature was affected by ground water and surface water inputs and withdrawals as well as from vegetation canopy, solar radiation, climate impacts, and sediment thickness. Stream discharge was measured with a Marsh McBirney Flo-Mate 2000™ current velocity meter and standard USGS area-velocity method at all sites. Instantaneous flow was measured at 63 locations (19 mainstem locations, 26 tributaries and irrigation return flows, and 18 irrigation withdrawals) to develop a water balance and groundwater influence between model reaches. The temperature model was divided into ten reaches; as a result, groundwater abstraction or inflow was combined at the reach breaks for model input data. Ground water gain/loss was validated for the study reach from a previous ground water / surface water study compiled by WET in which included mainstem Jefferson River flow monitoring from above the Parrot Canal to below the Willow Spring confluence. Based on these data collected in 2005, a course level water balance was developed. The 2005 water balance identified similar gaining and losing reach locations as determined in this 2009 study; however it should be noted that flow conditions and monitoring reaches were different for each study. Rating curves were developed for each reach break by determining a power equation exponent from the gaging station data and by solving for a reach-specific coefficient based on field-measured wetted width, velocity, flow, and depth for each mainstem flow measurement. The Upper Jefferson River temperature model incorporated several components of ground water and/ or surface water hydraulic calculations and adequately described conditions in the river corridor.