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A simulation-optimization model which incorporates the flow and contaminant transport simulation model within an optimization program helps in designing the best satisfactory bioremediation system. For the effective bioremediation system design, the groundwater flow and contaminant transport should be simulated at various time steps. For optimal design, groundwater flow and transport modelling is coupled with optimization techniques of Particle swarm optimization. Biodegradation process is simulated by incorporating an instantaneous reaction model. Decision-makers require adequate information on these interactions in order to formulate sustainable water resources development strategies. A successful groundwater management requires precise information on groundwater quantity and quality, its renewability and the hydrogeological structure of the subsurface formation. Differential evolution (DE) is a method that optimizes a problem by iteratively trying to improve a candidate solution with regard to a given measure of quality. In this book in 2nd section transmissivity (T) values are estimated by coupling the differential evolution optimization technique with FEM simulation model.