The geomorphological disposition of (para/peri) glacial landforms, elemental geochemistry, and optical chronology of the relict lake sediment in the Southern Zanskar ranges, northwest Himalaya are used to understand the relationship between glacial dynamics and the lake sedimentation during the mid-Holocene climate variability. Following the Last Glacial Maxima (LGM), pulsating deposition of outwash gravels until the early Holocene overwhelmed the Zanskar valley. The obstruction of Tsarap Chu (chu = river) by alluvial fans during the mid-Holocene led to the development of Padum Lake. In the present study, cirque glacier moraines representing three minor glacial advances were mapped along with sedimentological details and dated using Optically Stimulated Luminescence (OSL) dating technique. The oldest cirque glacier advance - Padum Cirque moraine-3 (PDCm-3) is dated to 11.4 ± 0.9 ka. The succeeding advance (PDCm-2) is dated to 5.3 ± 0.6 and 4.8 ± 0.8 ka whereas, the younger cirque glacier advance (PDCm-1) remains undated. The mid to late Holocene climate variability inferred using major and trace element geochemistry of the relict Padum lake sediments supported by optical chronology indicates six centennial to millennial-scale climatic phases. The prominent warmer phases are represented by decreased mineralogical fine grain flux (low K/Ti, Fe/Si, and Al/Si) with a corresponding increased coarse grain flux (higher Ti/Al and Sr/Al ratios). These phases are dated between 5.9 and 5.5 ka (phase-I), 3.8 and 3.4 ka (phase-IV), and 2.8 and 2.5 ka (phase-VI). The increased mineralogical finer fraction (higher K/Ti, Fe/Si, and Al/Si) between 5.5 and 5.1 ka (phase-II) and 3.4 and 2.8 ka (phase-V) indicate reduced meltwater flux during cooler phases. The intervening phase-III (5.1–3.8 ka) is characterized by increased mineralogical coarse grain flux (decreasing K/Ti, Fe/Si, Al/Si) suggesting gradual warming. The oscillatory climate at millennial scale was further used to understand glacier dynamics. The PDCm-2 advance in the lake record corresponds to the first major cooling (5.5 and 5.1 ka; phase-II) and continued until ∼3.8 ka. Using geochemical data of lake record, a major recession is inferred after 3.8 ka that persisted until around 3.4 ka (phase-IV). Similarly, the undated younger cirque glacier advance (PDCm-1) is assigned to the second cooling event (3.4 and 2.8 ka; phase-V). Thereafter, the cirque glaciers receded, most likely under increasing dryness and fluctuating climate (2.8–2.5 ka, phase-VI). After ∼2.6 ka, the development of ice-wedge pseudomorphs indicates the onset of permafrost conditions that degraded after ∼2.5 ka implying an increase in air temperature. The lake sedimentation terminates with the deposition of multiple younger alluvial fan facies. The climate variability shows a close correspondence with regional climate records suggesting that marginal glacier advancements were triggered by enhanced moisture via atmospheric rivers and cooler winter temperatures. The study highlights the potential of relict lake sediment in association with para- and peri-glacial landforms to reconstruct the pattern of minor glacier responses to climate variability during the Holocene.