Hydraulic Water Retaining Structures (HWRS), such as dams, weirs and regulators are important projects and necessary for water management. Seepage analysis results under HWRS substantially influences the design of HWRS. One of the biggest challenges in design of HWRS is to determine the accurate seepage characteristics with complex flow conditions, and simultaneously to find the optimum design considering safety and cost. Therefore, this study concentrates on developing a linked simulation-optimization (S-O) model for complex flow conditions. This is achieved via linking the numerical seepage simulation (Geo-Studio/SEEPW) with the Genetic Algorithm (GA) evolutionary optimization solver. Since, a direct linking of numerical model with optimization model is computationally expensive and time consuming, well-trained Support vector machine (SVM) surrogate models are linked to the optimization model instead of a numerical model within the S-O model. The seepage characteristics of optimum design obtained by S-O are evaluated for accuracy by comparing these with the numerical seepage modelling (SEEPW) solutions. The comparison, in general, shows good agreements. Accordingly, the S-O methodology is potentially applicable for providing safe, efficient and economical design of HWRS constructed on a complex seepage flow domain.