The higher requirements are put forward for the design of bridge deck drainage in the water source protection area. The design process of the bridge deck runoff collection and treatment system across the water source protection area is illustrated through the engineering design example. The comparison scheme for the bridge deck runoff collection and treatment system of the super large bridge is put forward. At the same time to solve the problems of drainage and environmental protection, the reasonable design suggestions for the bridge deck longitudinal slope and structural form are proposed, which plays a certain reference role for the design of similar projects.