The modern sediments in the Cataraqui River lagoon and marsh (Kingston, Ontario) consist of mixtures of organic material and clayey silts, the organic content of which increases as water depth decreases; gyttjas are accumulating in the deeper water parts of the lagoon, whereas peat is the dominant sediment in the very shallow water portion of the lagoon (< 0.7 m) and in the adjacent marsh. Cores show that one partial (modern) and two complete depositional cycles (gyttja passing upwards into peat) have formed within the last 4000 years. The contact between cycles (gyttja over peat) is abrupt. These cycles are interpreted as resulting from fluctuations in the level of Lake Ontario about the long-term rising trend. Radiocarbon dates show that relatively low levels prevailed from 4100 to 3300 BP and from 2300 to 1900 BP; rapid rises in water level, which are indicated by the abrupt contact between cycles, occurred at 3300–3100 BP and some time between 2000 and 1500 BP. These water-level changes are synchronous with those shown by other studies in Lake Ontario and with century-scale paleoclimatic events. The high stands correlate with wet periods, and perhaps also with warm periods in the eastern part of the Great Lakes basin, but an inverse relationship between precipitation and temperature in the western Great Lakes suggests that the Great Lakes basin does not respond uniformly to climatic changes.