Ecological shifts in shallow lakes from clear-water macrophyte-dominated to turbid-water phytoplankton-dominated are generally thought of as rapid short-term transitions. Diatom remains in sediment records from shallow lakes in the Prairie Pothole Region of North America provide new evidence that the long-term ecological stability of these lakes is defined by the legacy of large regime shifts. Here we examine the modern and historical stability of eleven shallow lakes. Currently, four of the lakes are in a clear-water state, three are consistently turbid-water, and four have been observed to change state from year to year (transitional). Lake sediment records spanning the past 150-200 years suggest that: 1) the diatom assemblage is characteristic of either clear or turbid lakes; 2) prior to significant landscape alteration, all of the lakes existed in a regime of a stable clear-water state; 3) lakes that are currently classified as turbid or transitional have experienced one strong regime shift over the past 150-200 years, and have since remained in a regime where turbid-water predominates; and 4) top-down impacts to the lake food web from fish introductions appear to be the dominant driver of strong regime shifts, and not increased nutrient availability. Based on our findings we demonstrate a method that could be used by lake managers to identify lakes that have an ecological history close to the clear-turbid regime threshold; such lakes might more easily be returned to a clear-water state through biomanipulation. The unfortunate reality is that many of these lakes are now part of a managed landscape and will likely require continued intervention.