Riparian zone hydrology is dominated by shallow groundwater with complex interactions between groundwater and surface water. There are obvious relations of discharge and recharge between groundwater and surface water. Flood is an important hydrological incident that affects groundwater quality in riparian zone. By observing variations of physical and chemical groundwater indicators in riparian zone at the Kouma section of the Yellow River Wetland, especially those took place in the period of regulation for water and sediment at the Xiaolangdi Reservoir, relationship between the groundwater quality in riparian zone and the flood water quality in the river is studied. Results show that there will be great risk of nitrogen, phosphorus, nitrate nitrogen and organic matter permeating into the groundwater if floodplain changes into farmland. As the special control unit of nitrogen pollution between rivers and artificial wetlands, dry fanning areas near the river play a very important role in nitrogen migration between river and groundwater. Farm manure as base fertilizer may he an important source of phosphorus leak and loss at the artificial wetlands. Phosphorus leaks into the groundwater and is transferred along the hydraulic gradient, especially during the period of regulation for water and sediment at the Xiaolangdi Reservoir. The land use types and farming systems of the riparian floodplain have a major impact on the nitrate nitrogen contents of the groundwater. Nitrogen can infiltrate and accumulate quickly at anaerobic conditions in the fish pond area, and the annual nitrogen achieves a relatively balanced state in lotus area. In those areas, the soil is flooded and at anaerobic condition in spring and summer, nitrogen infiltrates and denitrification significantly, but soil is not flooded and at aerobic condition in the autumn and winter, and during these time, a significant nitrogen nitrification process occurs. In the area between 50 m and 200 m from the river bank, which is the efficient microbial nitrogen purification unit, nitrification-denitrification is intensive. Farm manure is an important source of organic matter loss at the artificial wetlands. Floodplain has sandy soil texture, with high infiltration capacity and low water and fertilizer conservation ability. Such features are prone for the loss of surface soil nutrition and organic matter if agricultural activities taken place in these areas change the land use of wetlands and apply extensive fertilizer. The infiltrated nutrition elements and organic matter can pollute the groundwater and the river. Compared with the losses of nutrition element and organic matter caused by surface runoff, the infiltrated process is even more prominent. As typical floodplain groundwater-river ecotone, the area between 50 m and 200 m from the river bank is a momentous pollution purification unit. Rational protection for this region is critical for the conservation of water quality in the river and groundwater.