The roles of both landscape alteration and in-lake processes need to be considered in conservation strategies for shallow lakes in the prairie regions of North America. Here we focus on shallow lakes in west-central Minnesota, USA, highlighting the long-term ecological history and response to known landscape changes of a clear-water, macrophyte-dominated, shallow lake. Contemporary limnological data suggest the aquatic ecosystem has been very stable and fishless for the last ~15 years. Sediment proxies for primary production and ecological change confirm that a stable ecosystem likely prevailed for the last ~200 years. However, sedimentary indicators of catchment erosion detail a distinct response to land-use change during the conversion of native grassland to agricultural land, and following establishment of a protected waterfowl production area (WPA) around the lake. Post-WPA, the rate of sediment accrual decreased dramatically within 5–10 years and sources of organic matter were similar to those of the pre-settlement period. The aquatic ecosystem has been able to withstand nutrient enrichment and allochthonous inputs because stable trophic interactions have likely been in place for more than 200 years. We conclude that lack of hydrologic connectivity and isolated, small catchments are important factors in the promotion of clear-water shallow lake ecosystems, mainly because they prevent colonization by fish and associated ecological consequences. This study highlights the importance of managing both the landscape and in-lake processes to maintain stable, clear-water, shallow lakes.