Groundwater is one of the most important water sources but it is often not far away from pollution. One source of pollution is leakage from polluted streams such as open drains. The effect of open drains on groundwater quality has become an essential issue. This study aims to use different lining materials to minimize the seepage from open drains to protect groundwater. MODFLOW is used to investigate flow and contaminant transport and to evaluate efficiency of different lining materials. A hypothetical case study is used to assess different lining materials such as clay, bentonite, geomembranes and concrete. The results showed that decreasing the conductivities of lining materials reduced the extension of the contaminate. The extension of contaminants was reduced by 43, 89.6, 91.4 and 93% compared with the base case when drains were lined by clay, bentonite, geomembranes and concrete, respectively. Also, cost analysis of lining materials was done to detect the best lining material. Lining using geomembranes reduced contaminant extension at low cost compared with concrete, which reduced contaminant extension at double the cost. This reveals that the geomembranes represent the preferred material to protect groundwater from drain seepage due to its high durability and low cost compared with concrete.