Shallow lakes are susceptible to catastrophic regime shifts characterised by the presence or absence or macrophytes. However, the long-term controls on macrophyte succession in shallow lakes are incompletely understood. To investigate this, we analysed multiple sediment proxies in Lake Rotcze (Eastern Poland), a small, shallow and densely macrophyte-covered lake to (1) reconstruct the ‘reference conditions’ (sensu WFD) and development of the lake in recent centuries, (2) compare historical evidence with the sedimentary record, and (3) identify the natural and anthropogenic drivers of macrophyte succession. Before the twentieth century, conditions in the lake may be referred to as ‘reference conditions’. Subsequently forest clearance in the catchment resulted in lower water transparency, but concurrent catchment drainage lowered water levels and increased macrophyte development. Since 1950 elevated nutrient supply and climatically driven increases in water levels led to the deterioration of water transparency and partial macrophyte withdrawal. At the end of the twentieth century lake-level drawdown led to low phytoplankton biomass and clear water creating a novel ecosystem where macrophytes invade the whole lake. These patterns suggest that both natural and anthropogenically induced water level fluctuations have been critical drivers of macrophyte development.