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Summary 1. Lake Victoria endured multiple stresses over the past century including population growth, increased cultivation of land, meteorological variability, resource extraction, intensive fishing, introduction of exotic species and more recently climate warming. These stressors became manifest through a fundamental and rapid change in the fish community and fishery in the early 1980s and visible eutrophication. However, the relation of these two phenomena and the possible interaction of the multiple stressors have been difficult to establish because of the temporally fragmented nature of the environmental data. 2. Comprehensive limnological observations from the 1960s were repeated in the 1990s and established the eutrophication of the lake, but these do not provide insight to the time course of when changes in trophic state occurred. Comprehensive fishery catch data from 1965 to the present provide a time course of the change in community composition and yield but cannot be correlated in time with discontinuous and sparse limnological data to determine possible cause–effect relationships. 3. Palaeolimnologic studies were conducted on three cores, two offshore and one nearshore, to establish a time course for the eutrophication of the lake that can be related to time‐based data on the fishery. In the 1920s, the cores recorded an increase in nitrogen content of the sediments, but there was no significant response in the paleo‐productivity indicators of biogenic Si deposition and change δ 13 C of deposited organic matter. Phosphorus deposition began to increase in the 1940s in all three cores after which biogenic Si deposition increased steadily over time. Responses in δ 13 C of organic matter begin in the 1960s at the coring sites. In the 1970s, the δ 13 C of organic matter at the nearshore site increased nearly 3‰ in a 10‐year period likely as a response to a dramatic increase in internal P loading caused by spreading anoxia. 4. Nile perch, the large predatory fish introduced in 1954, had become established through much of the lake at low abundances by the 1970s. In 1980, the catch of this fish began to increase, and by the end of the decade, the Lake Victoria fishery was the largest lake fishery in the world; and Nile perch dominated the catch. While catches of some other fishes also increased, the endemic haplochromines suffered a catastrophic decline in abundance and loss of biodiversity. 5. The detailed chronostratigraphies for these sediment cores established that the major changes in the trophic condition of the lake were accomplished prior to the change in the fish community and that the increased primary productivity of the lake likely contributed to the increased fish catches after 1980. The increased algal abundance also would have greatly reduced visibility and facilitated the emergence of Nile perch as the dominant top predator. 6. Thematic implications : multiple stresses were present in Lake Victoria over several decades, but transition to a new ecosystem state with a transformed food web and highly productive algal community may have been triggered by a period of low wind stress and then generally warming climate since the 1970s. Unless phosphorus loading is stabilised or reduced, the ecosystem’s diversity and balanced productivity will not recover, and other state transitions may occur to the detriment of the lake and its riparian populations.