Having produced tremendous social benefits since its operation, the middle route project of the South-to-North Water Transfer has attracted increasing demands from areas along the route and in the Beijing-Tianjin-Hebei region. Maintenance of the channel with water cutoff would bring about risks; hence repairing the channel lining board and in the meantime maintaining water delivery poses a difficulty for engineers. Complicated seepage control measures were arranged under the lining board in some excavated channels with high-level groundwater. In emergency maintenance of the lining board at bottom or at deep by constructing cofferdam in the presence of water conveyance, engineers are faced with anti-floating problems and seepage failure possibly caused by the water level difference inside and outside the cofferdam foundation pit. In view of this, in line with the design of seepage control and cofferdam layout, we propose a seepage control plan for the cofferdam foundation pit: to block the permeable pipe of the canal foundation outside the cofferdam foundation pit, and to install water pump around the pit for drainage. Simulation results of the three-dimensional seepage field demonstrate that the horizontal permeability gradient and the water inflow of the foundation pit can be reduced remarkably by using the plan, hence ensuring the safety of foundation pit. The research finding offers theoretical basis and technical support for the emergency maintenance in the presence of water delivery.