Lake level regulation is commonly used to manage water resources and mitigate flood risk in watersheds with linked river-lake systems. In this study, we first assess exposure, in terms of both population and land area, to flooding impacts in the Yahara Watershed’s chain of four lakes in southern Wisconsin as affected by minimum lake level management. A flooding exposure assessment shows that the areas surrounding the upstream lakes, Mendota and Monona, have dense urban areas with high populations that are exposed to flooding; Waubesa has low elevations along its lakeshore, resulting in a large potential flooding area; and the most downstream lake, Kegonsa, has a large area of surrounding cropland that is exposed to flooding but impacts a limited population. We then use a linked modeling framework of a land surface model (Agro-IBIS) and a hydrologic-routing model (THMB) to simulate daily lake level over a study period of 1994-2013 in the Yahara Watershed with different minimum lake level management strategies. Modeling results show that the peak lake levels and corresponding exposed land area and population to flooding will decrease under a lower target minimum lake level. However, at the same time, the number of days that the lake level is below winter minimum will increase, which may adversely affect ecosystem health. In addition, our sensitivity analysis indicates that reducing target minimum lake levels will help mitigate flood risk in terms of both flood magnitude and frequency. Nevertheless, this must be balanced against the need to maintain adequately high lake levels for ecosystem services and recreational functions of the lakes.