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Sediment sequences in Lake Qinghai spanning the past 100 years were explored to assess the effects of changes in local land desertification, dust input and agriculture on sediment deposition in different parts of Lake Qinghai. Three short sediment cores (QH01, QH02, QH07) were collected from the main lake and one sediment core (Z04) from a sublake (Lake Gahai) of Lake Qinghai, China, during 2012 and 2013. The concentrations of Fe, Mn, Al, Rb, Ti, Ca, and Sr were analysed to determine the effects of historical and regional anthropogenic activities in the Lake Qinghai catchment from 1910 to 2010. The elemental concentrations in the sediment cores ranged from 1.85 to 2.79% for Fe, 397 to 608 μg/g for Mn, 3.04 to 5.64% for Al, 13.5 to 19.7 μg/g for Rb, 0.171 to 0.268% for Ti, 9.43 to 13.9% for Ca, 652 to 1020 μg/g for Sr, and 0.049 to 0.075% for P. Good correlations were found between the concentrations of Fe, Mn, Al, and Rb, and the Ti/Al ratios in the sediments suggest that these elements share a similar source. The enrichment factors (EFs) of Ti [EF(Ti)] and P [EF(P)] in each core were utilized to reflect variations in anthropogenic activities from 1950 to 2010. EF(Ti) ranged from 1 to 1.17 in QH01 and QH02, reflecting the variation of land desertification areas in the Buha River catchment from 1950 to 2010. The EF(Ti) showed positive linear correlations with the variation in cropland area in Gangcha County, suggesting that agricultural activity in the Quanji River and Shaliu River catchments was enhanced from 1950 to 2010. The sediment records showed similar biogeochemical changes in most lakes and bays in China, indicating that the intensity of changes in anthropogenic activities was caused by national policy enforcement from the 1950s to 2010. EF(Ti) can serve as a tracer for anthropogenic activities in Lake Qinghai, with the anthropogenic activities in different parts of the Lake Qinghai catchment represented in the homologous sediments from parts of Lake Qinghai over the past 100 years. The variation of EF(P) increased from 1 to 1.55 from deep layer to upper layer in all sediment cores, reflecting the increased fertilizer input and tourism activity from 1980 to 2010, a period during which the lake was evolved into a eutrophic lake.