Lake restoration efforts in Iowa have attempted to incorporate groundwater contributions to the nutrient (Nitrogen and Phosphorus) budget. Analytic element models, with their ability to model both surface water and groundwater, are well suited to this application. In this example, GFLOW 2000 was used to simulate regional groundwater flow, estimate groundwater discharge to (and recharge from) Clear Lake, construct nutrient budgets, and identify source areas for nutrients. Clear Lake, located in north central Iowa, supports a $30 million/yr recreation and tourism industry. Water quality has declined during the past 30 years, coincident with an increase in Total P concentration from about 60 ppb to 190 ppb. It is the third largest of 34 natural lakes in the state and has a surface area of 1,450 ha, a maximum depth of 5.8 m, and an average depth of 2.9 m. The lake watershed lies within the Algona-Altamont moraine complex, covers 4,832 ha, and is composed of 59 percent row cropland. Hydraulic head, K, and nutrient concentration data were obtained from 33 nested piezometers. Streams, drainage ditches, and drainage tiles were included within a regional model domain of 50,000 ha. A solution was obtained with the lake represented as a zone of high hydraulic conductivity (K ~ 0.1 m/s) within a fractured till-dominated domain (K = 5 x 10-5 m/s). Results of conjunctive groundwater/ surface-water simulations indicate Clear Lake is a flow-through lake and receives groundwater discharge everywhere (about 8000 m3/d) except on the eastern side, where the lake recharges groundwater. Nitrate-N is removed by denitrification prior to entering the lake. About 1.4 kg/day of Total P enters the lake from groundwater, which comprises only 7 percent of the annual P budget of the lake. Particle tracking suggests that most P in groundwater emanates from cropland near the shoreline and that the outer margins of the watershed will provide P to the lake for the next several decades.