A central topic in nature conservation and ecological restoration is the potential of ecosystems to recover after the reduction of negative anthropogenic impacts. Often, protracted delays in biotic response to abiotic change have been observed. We analysed a unique long-term data series in Lake Fure, Denmark, spanning the transformation from pristine environmental conditions in the early 1900s through a period (1920–1970) of eutrophication – from accelerating sewage input of phosphorus (P) – and subsequent re-oligotrophication after sewage cleaning (1970–2015). We examine time delays between P inputs, in-lake P concentrations and the richness and composition of submerged macrophyte communities. Lake P concentration exhibited decade-long delays in response to periods of increasing or decreasing P inputs. It took 40 years and a 25-fold increase in P input before P concentrations suddenly took off in the 1960s, reflecting profound sediment accumulation. Following reduced P input from c. 1970, it took 5 years before P concentrations showed the first signs of a decline. In 2014, water P concentration was still markedly higher than in 1931, despite much lower P inputs, because of elevated sediment release. Fifty years of eutrophication led to a reduction in aquatic macrophyte richness from 36 species to 12. Species’ responses were closely related to their growth strategy and depth distribution. Deep-growing mosses, charophytes and short angiosperms disappeared, while tall angiosperms survived and pollution-tolerant macroalgae colonized and spread. Subsequently, 45 years of oligotrophication led to clearer waters, macrophyte richness recovering to 28 species and some charophytes and short angiosperms reappearing. Dominance of pollution-tolerant macroalgae persisted, however. Change in species dominance takes longer than colonization by new species. Synthesis. Time delays of P concentrations, water clarity and macrophyte richness and composition were long and complex. Neglecting growth strategies of species makes application of extinction debt and colonization credit concepts dubious, because numbers of oligotrophic species decrease and eutrophic species increase concomitantly during eutrophication and vice versa during oligotrophication. Although the original high species richness may be attained, it is unlikely that the original species composition is restored because many oligotrophic species have vanished from the regional species pool.