The selective withdrawal system (SWS) has often been used to alleviate downstream temperature pollutions and in-reservoir unacceptable oxygen concentrations whilst increasing hydropower energy generation. The aim of this study is to a) design the optimal locations of intakes in SWS, and, b) derive optimal parameterized selective withdrawal operation rules. The integration of water quality and quantity aspects to meet long-term environmental services and economic benefits is challenging. The main challenge lies in coupling search-based optimization algorithms with a numerical hydrodynamic and water quality simulation model (i.e., CE-QUAL-W2). To cope with the computational burdens of CE-QUAL-W2, surrogate models have been developed to represent the dynamics of temperature and water quality according to various SWSs. The surrogate models and the hydropower energy computation module were coupled with a multi-objective particle swarm optimization algorithm in an adaptive surrogate-based simulation–optimization framework (ASBSOF). The ASBSOF is applied in Karkheh reservoir, Andimeshk, Khuzestan, Iran, to address problems a and b. The results indicate that the optimal SWSs provide the advantage of sustainable management to balance the energy generation whilst minimizing environmental damages.