Catchment-scale exports of organic and inorganic carbon plays an important role in affecting the lake sediment carbon burial. Inorganic carbon cycling in Karst landscapes is sensitive to human activities due to the rapid kinetics of carbonate dissolution. As with intensive watershed development, the source, content and burial loading of organic and inorganic carbon in Karst region may show a synchronous change. This study selected two medium-sized lakes (Lake Changhu and Lake Yuehu) with contrasting land uses patterns in the Shilin Karst area of central Yunnan for sediment surveys. With the proxies analyses for soil erosion (i.e. magnetic susceptibility (MS)), catchment allochthonous input (C∶N ratio), lake hydrology (particle size), nutrient levels (total phosphorus and nitrogen) and primary production (i.e. algal pigments), together with monitoring data and historical records, the history of limnological changes and catchment development over the last century for both lakes were reconstructed. Furthermore, long-term variation and synchronic pattern of sediment organic carbon (OC) and inorganic carbon (IC) burial in the context of catchment development were quantified. The sediment MS signal recorded the fluctuation in soil erosion intensity and a general pattern of long-term nutrient enrichment in both lakes. In Lake Changhu, with a higher land cover of forest (33.43%), the bulk and organic C∶N ratios were positively related with the MS signal (r=0.95 and 0.89, P < 0.001) but showed a negative relationship with sediment inorganic and organic carbon content (r=-0.94, P < 0.001 and -0.52, P=0.01), respectively, reflecting a significant impact of catchment carbon input. In Lake Yuehu, with a current land cover dominated by the cropland (60.98%), the bulk and organic C∶N ratios were negatively related with the MS signal (r=-0.54, P < 0.01 and -0.67, P < 0.001) and the bulk C∶N ratio showed no relationship with the sediment inorganic content (P=0.15), reflecting that the cropland expansion may have enhanced lake eutrophication and autochthonous input. In both lakes, nutrient enrichment and algal production enhanced the rapid OC accumulation. Additional analyses showed that there existed a significantly synchronous change between OC and IC content in Lake Changhu (r=0.54, P < 0.001) but not in Lake Yuehu (P=0.20, P>0.05). In both lakes, sediment loading was positively related with bulk C∶N ratio (r=0.48 and 0.45, P≤0.001), and there also existed a significantly synchronous change between OC and IC loadings (r=0.72 and 0.85, P < 0.001). Furthermore, the IC burial rate was significantly higher than that of OC in Lake Changhu, while IC consistently lower than OC in the nutrient-rich Lake Yuehu, reflecting differential forcing of vegetation degradation and lake eutrophication. With the intensive development in watershed, forest degradation can reduce the loading of catchment carbon export, while agricultural expansion and eutrophication would promote the growth of algae and the OC accumulation rate. Therefore, land use and lake nutrient levels can significantly impact the long-term trajectory and synchronic variation of sediment OC and IC burial. Thus, IC cycling should be considered in the regional assessment of carbon stock in karst areas.