Sedimentary facies and micro-fossil analyses, and AMS 14 C dating were performed in order to reveal the water-level fall events and draining process of the lake (Paleo-Kathmandu Lake) that existed in the past in the Central Nepal Himalaya. The sedimentary facies change from the lacustrine Kalimati Formation to the deltaic Sunakothi Formation in the southern and central Kathmandu basin, and the abrupt and prominent increase of phytoliths Bambusoideae and Pediastrum, and contemporaneous decrease of sponge spicule and charcoal grains around 48 and 38 ka support the lowering of water level at these times. According to the pollen analysis, both events occurred under rather warm and wet climate, thus supporting that they were triggered by tectonic cause and not by climate change. The first event might be linked to a possible occurrence of a large earthquake with an epicenter in the vicinity of the PaleoKathmandu Lake. The occurrence of a mega landslide in Langtang area close to the north of the Kathmandu Valley producing pseudotachylite dated at 51 ± 13 ka could be linked to this earthquake. Finally, the water was completely drained out from the remnant lake at the central part of the Kathmandu basin by ca.12 ka.