The headwaters of the Tigris River basin in Iraq is controlled by Turkey due to a series of dams constructed over the last few decades. Since Total Dissolved Solids (TDS) in the Tigris River within Baghdad and downstream cities can reach 1000 mg/L exceeding both drinking water and irrigation guidelines, a hydrodynamic and water quality model, CE-QUAL-W2, of the river was developed to understand how changes in flow affect TDS downstream. A model of 880 km of the Tigris River from Mosul Dam to Kut Barrage including Tharthar Lake was constructed for 2009. Model development was challenging due to a lack of in-situ measurements for calibration. Comparison of flow measurements and model predictions at downstream locations agreed well with field measurements, with model flow errors generally less than 2%. We evaluated the effect of changing upstream flow conditions on total dissolved solids concentrations in the Tigris River in order to see how headwater flow control affects TDS. A sensitivity study suggested that increasing upstream river flow by 15% results in about a 5% decrease in TDS concentration. It was recommended to maintain an average annual flow in the Tigris River within Baghdad above 420 m3/s to keep total dissolved solids concentration below 500 mg/L and to strictly control flows through Tharthar Lake and irrigation return flows into the mainstem of the Tigris River.