Due to the dual influence of climate change and human activities, the water cycle patterns in the lakesheds of the Yunnan karst plateau are undergoing significant changes, leading to increasingly prominent ecological issues. In the history of Lake Yangzong, an artificial water-diversion channel was excavated, altering the lake basin structure. Human activities have intensified, posing severe challenges to water resource supply and water security in recent decades. To investigate the significant increase in human activities, the temporal and phase changes, and the resulting transformation of the water and carbon cycles in the Lake Yangzong basin, we applied X-ray fluorescence spectroscopy (XRF) to scan elements continuously in a 10.2 m sediment core from this lake. By combining correlation analysis, principal component analysis (PCA), core chronology, and total organic carbon (TOC) content, we reconstructed the historical sequence of geochemical element contents in the Lake Yangzong catchment over the past 13,000 years. The results show that PC1 and PC2 contribute 78.4% and 10.3%, respectively, suggesting that erosion intensity is the main factor influencing the lake sedimentation process. From 13,400 to 680 cal a BP (calibrated years before the present), the sedimentation process in Lake Yangzong was mainly controlled by climatic conditions, with vegetation degradation during cold periods and relatively high erosion intensity in the watershed. During the Yuan dynasty, a province was established by the central government in Yunnan, promoting settlement and attracting a large number of immigrants from other provinces to Yunnan. Human activities in the Lake Yangzong basin began to intensify, surpassing natural changes and becoming the dominant force influencing the sedimentation process. In the Ming and Qing dynasties, the population and cultivated land area in Yunnan further increased, resulting in the significant exacerbation of erosion and soil loss in the watershed due to vegetation destruction. In the year 1388, the Tangchi Canal was excavated, transforming Lake Yangzong to an outflow lake, causing Ca2+ to be lost through the Tangchi Canal and preventing the formation of precipitation due to oversaturation. The research results indicate that human activities in the Lake Yangzong area have intensified since the Yuan dynasty, leading to increased erosion intensity. The excavation of the outflow canal transformed Lake Yangzong from an inland lake basin into an outflow state, simultaneously generating a significant transformation in the water and carbon cycling patterns in the watershed.