Southeast Asia contains a major portion of wetland areas of international significance, but only 14% of these wetlands are under protection. Inle Lake is the second largest freshwater body in Myanmar and the most important for its environmental, economic, and agricultural values. However, the lake is seriously threatened by anthropic activities as they are dramatically decreasing its open water surface. While water-quality studies have assessed the presence of nutrients and contaminants, little is known about the sediment quality. Therefore, the overall objective of the present study was to analyse the natural sedimentation patterns and the anthropogenic disturbances in this lake. To this end, both grab and core sediments were investigated by combining mineralogical, morphological, and geochemical analyses, and their composition was compared to the composition of rocks and soil from the watershed. Mineralogical data indicate that sediment samples collected at or near the main inflow, and at the outflow show a lower abundance (about 43%) of calcite, which generally increases with depth in sediment cores, reaching more than 90% in the centre of the lake. Lower calcite contents correspond to higher percentages of other minerals. These findings allow us to clearly distinguish the allogenic (quartz, mica/illite, kaolinite, and detrital calcite) from the endogenic (mostly calcite) minerals, as confirmed by the soil and rock mineralogy. The origin of the mineral contents at the different sites is further supported by the observation of the grain morphology and composition. The most abundant metal in the lake sediments is Ca, in agreement with the high calcite content. Following in order of abundance are Al, Fe, and K, which are connected to the detrital input to the lake. In the rock and soil samples, the most abundant trace element is Mn, which is significantly correlated with many other trace elements (e.g., Co, Cr, Cu, Ni, V, Zn, and As), suggesting their common lithogenic origin. Similarly, in the lake sediments, the trace elements Co, Cr, Cu, Ni, Pb, V, Zn, and As display fairly homogenous concentration ranges, in the order of tens of ppm, and are strongly correlated with the detrital minerals (mica, kaolinite, and quartz) and negatively correlated with the calcite content. The mineralogical and elemental distribution in the lakebed area and with depth in the sediment cores allowed us to identify the increased soil and bedrock erosion as a major anthropogenic impact to the lake. The sedimentation disturbance is especially evident at the main inflow, the Nanlit stream, which has caused the development of a large alluvial fan, visible in satellite images. This large sediment input is likely to have accelerated the decrease in open water surface and in depth of this shallow lake. Additionally, when the measured concentrations of Potentially Toxic Elements were compared to consensus-based Sediment Quality Guidelines (SQGs), it was shown that As, Cr, Cu, Ni, Pb, and Zn often exceeded the threshold effect concentration (TEC), and that Cr, Ni, and Pb sometimes exceeded the probable effect concentration (PEC). On the other hand, Enrichment Factors (EFs), calculated with respect to soils of the watershed, showed minimal enrichment and indicated that the potential toxicity effect was primarily a result of detrital sedimentation outpacing carbonate sedimentation. Sediment characterisation allowed us to obtain a better understanding of lake dynamics and environmental impacts, which is fundamental in achieving effective management and maintenance of the ecological character of Inle Lake, in line with the objective set by the Ramsar Convention for wetlands of international relevance.