Water quality and hydrodynamic models of proposed hydroelectric projects in Guyana and in Peru were developed to help evaluate the environmental impacts on water quality and greenhouse emissions of these new reservoirs. The public domain 2-dimensional (longitudinal-vertical) hydrodynamic and water quality model, CE-QUAL-W2, was chosen for these projects. Modeled state variables included water surface elevation, velocities, temperature, dissolved oxygen, labile/refractory dissolved organic matter, labile/refractory particulate organic matter, CBOD, algae, PO4-P, NH3-N, NO3-N+NO2-N, suspended solids, pH, alkalinity, Total inorganic C, dissolved CO2, and sediments. CO2 fluxes from the reservoirs were also estimated. New state variables, methane (CH4) and hydrogen sulfide (H2S) constituents were added to the model including the processes of anaerobic release from the sediments and reaeration. Water quality model simulations were conducted for low, average, and high flow years and included the river systems downstream of the proposed reservoirs. The impacts of reservoir upon dissolved oxygen, carbon dioxide, methane, hydrogen sulfide, temperature, algae, and carbon loads were evaluated. Atmospheric emissions of carbon dioxide were predicted for the reservoir and river downstream.