Multiple stressors to a shallow lake ecosystem have the ability to control the relative stability of alternative states (clear, macrophyte-dominated or turbid, algal-dominated). As a consequence, the use of remedial biomanipulations to induce trophic cascades and shift a turbid lake to a clear state is often only a temporary solution. Here we show the instability of short-term manipulations in the shallow Lake Christina (Minnesota, USA) is governed by the long-term state following a regime shift in the lake. During the modern, managed period of the lake, three top-down manipulations (fish kills) were undertaken inducing temporary (5–10 years) unstable clear-water states. Paleoecological remains of diatoms, along with proxies of primary production (total chlorophyll a and total organic carbon accumulation rate) and trophic state (total P) from sediment records clearly show a single regime shift in the lake during the early 1950s; following this shift, the functioning of the lake ecosystem is dominated by a persistent turbid state. We find that multiple stressors contributed to the regime shift. First, the lake began to eutrophy (from agricultural land use and/or increased waterfowl populations), leading to a dramatic increase in primary production. Soon after, the construction of a dam in 1936 effectively doubled the depth of the lake, compounded by increases in regional humidity; this resulted in an increase in planktivorous and benthivorous fish reducing phytoplankton grazers. These factors further conspired to increase the stability of a turbid regime during the modern managed period, such that switches to a clear-water state were inherently unstable and the lake consistently returned to a turbid state. We conclude that while top-down manipulations have had measurable impacts on the lake state, they have not been effective in providing a return to an ecosystem similar to the stable historical period. Our work offers an example of a well-studied ecosystem forced by multiple stressors into a new long-term managed period, where manipulated clear-water states are temporary, managed features.