We present a novel hybrid algorithm, integrating a genetic algorithm (GA) and constrained differential dynamic programming (CDDP), to achieve remediation planning for an unconfined aquifer. The objective function includes both fixed and dynamic operation costs. GA determines the primary structure of the proposed algorithm, and a chromosome therein implemented by a series of binary digits represents a potential network design. The time-varying optimal operation cost associated with the network design is computed by the CDDP, in which is embedded a numerical transport model. Several computational approaches, including a chromosome bookkeeping procedure, are implemented to alleviate computational loading. Additionally, case studies that involve fixed and time-varying operating costs for confined and unconfined aquifers, respectively, are discussed to elucidate the effectiveness of the proposed algorithm. Simulation results indicate that the fixed costs markedly affect the optimal design, including the number and locations of the wells. Furthermore, the solution obtained using the confined approximation for an unconfined aquifer may be infeasible, as determined by an unconfined simulation.