Shallow lakes, the most prevalent type of freshwater ecosystems, can shift between clear states with macrophyte dominance and turbid, phytoplankton-dominated states. Such transformations, commonly termed regime shifts, have gained increasing attention in recent decades. Of 1084 studies documenting regime shifts, only 28% investigated the consequences for ecosystem functions and services such as habitat (13%), carbon processing (4%), or nutrient retention (4%). Although there is general consensus that a clear macrophyte state supports a higher diversity of aquatic organisms than a turbid one, the effects of shifts on primary production, carbon burial, greenhouse-gas emissions, and nutrient retention remain ambiguous. Shifts between the two states also affect drinking-water quality and the recreational value of lakes, leading to conflicting management measures and potentially deteriorating natural functions. We call for more comprehensive studies on the effects of regime shifts on ecosystem functions in shallow lakes to guide their sustainable management.