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The Mekong River, one of the world’s great rivers, is facing the disruption of its sediment balance with anthropic reductions in its sediment load and resultant impacts on nutrient fluxes, aquatic ecology and evolution of its river channel, floodplain and delta. Using long-term monitoring data from 1993-2018, we estimated the temporal variability of sediment loads in Tonle Sap and Lower Mekong Rivers in Cambodia, assessing the sediment linkage between Tonle Sap Lake and Mekong River, which are connected by a seasonally reversing flow through the Tonle Sap River. We used data from three monitoring stations established in Cambodia in 1993, from the Mekong at Kratie (upstream) downstream to the Mekong at Chroy Changvar (just upstream of the Tonle Sap confluence), and the Tonle Sap River at Prek Kdam (about 40 km upstream of the Mekong confluence). We estimated the annual sediment in the main Mekong River was 72±38 Mt/yr at Kratie and 78±22 Mt/yr at Chroy Changvar from 1993-2018. Our calculated sediment load for the Lower Mekong River is lower than reported in older studies (prior to the 2000s), which is consistent with sediment trapping by dams on Upper Mekong mainstream and major tributaries built since 1993, and consistent with other recent estimates of sediment load on the Lower Mekong. Our analysis of water discharge and sediment concentration indicates that Tonle Sap Lake provided 0.65±0.6 Mt of sediment annually to the Lower Mekong River from 1995 to 2000. However, since 2001, Tonle Sap Lake has become a sink for sediment, accumulating an average of 1.35±0.7 Mt annually. Net storage of sediment in Tonle Sap Lake reduces the annual sediment transport to the Mekong delta, further compounding the effects of sediment delivery to the Delta resulting from upstream dam construction and instream sand mining.