The Mark Twain Lake Watershed in northeastern Missouri is the main source of water supply for 16 water districts in the region and is suffering serious water quality issues. A steady-state, analytical-element, groundwater flow model GFLOW simulation was constructed in the Mark Twain Lake watershed in claypan soils of northeastern Missouri including the Crooked Creek monitoring site. The objectives of the study were to establish a conjunctive surface water and groundwater model for central part of the Mark Twain Lake Watershed region using GFLOW. The near-field region consisted of 3,000 km2 area within a domain representing approximately 6,000 km2. The model was calibrated using 6 hydraulic head targets, 4 lake stage targets, and 5 baseflow flux targets by trial-and-error, UCODE, and PEST simulations. Parameters refined through the automatic technique yielded optimal values of 5 m/day for regional hydraulic conductivity for the model domain, 100 m/day for inhomogeneities (alluviual deposits along streams), and a recharge rate of 0.000195 m/yr (about 7% of mean annual precipitation). Model results indicated that Mark Twain Lake is a surface-water-dominated lake. Sixty-seven percent of the water arriving at the Mark Twain Lake is from streamflow and 22 percent from precipitation, whereas only 11 percent is from groundwater. The lake received about ten times more groundwater inflow (101,000 m3/day, 11 percent) than outflow (18,000 m3/day, 2 percent). More than ninety-eight percent of water moving out of the lake from is evapotranspiration (210,000 m3/day) and stream flow (731,000 m3/day), whereas only 2 percent (18,000 m3/day) is lost from groundwater. The groundwater flow and surface water discharge predicted by the GFLOW simulations probably reflect the strong influence of claypan soils in the study area, where overland flow comprises most of streamflow. According to the particle tracking results, NPS pollutants in groundwater are transported primarily downstream through highly permeable, alluvial channels. Groundwater inflow to the stream emanates only from a small zone immediately adjacent to the stream. These results suggest that the net effect of riparian buffers on NPS pollutants in the region could be increased by expanding buffers outward from the creek edge to the edge of the alluvial deposits along the valley.