Understanding pollen source and transport mechanisms is essential for interpreting marine pollen data, as factors like ocean currents and atmospheric circulation add complexity. Despite this, extensive studies using pollen sequences as proxies for river provenance and climate change are notably lacking. High-resolution palynological records from two Bay of Bengal (BoB) sediment cores offer insights into regional vegetation and climate history since MIS 3 (~48 ka). These records reveal that pollen and fern spore concentrations, which reflect land vegetation, decrease with distance from the coast, primarily representing inputs from the Ganges-Brahmaputra basins. The preservation of diverse pollen, particularly Castanopsis sp. and Euphorbiaceae, suggests a subtropical climate during the last glaciation, including MIS 3, with increased Pinus sp. pollen indicating a warmer climate and stronger ISM than in MIS 2. Herbaceous pollen, dominant during cooler, arid periods—particularly MIS 2 and the Last Glacial Maximum (LGM)—signals semiarid conditions and reduced monsoonal activity. Conversely, high arboreal pollen percentages during MIS 3 indicate a warm, wet climate with a robust ISM and stable sea levels. Principal component analysis (PCA) underscores the influence of transportation pathways and climatic conditions on pollen variations, with peaks in Pinus and broadleaved pollen during the Holocene reflecting intensified monsoon activity. Additionally, during MIS 1, increased monsoon intensity and warm interglacial conditions facilitated the expansion of tropical–subtropical forests, high sedimentation rates, and diverse ecosystems. Significant shifts in pollen records around ~40.5 ka and ~12 ka further reflect intensified hydrodynamic forces and heavy precipitation, signaling strong ISM activity. However, short-term humidity changes do not align with millennial-scale climatic cycles, suggesting that complex factors such as Intertropical Convergence Zone (ITCZ) shifts and global ice volume influenced regional precipitation. This study, therefore, provides a comprehensive view of past climate and vegetation dynamics in the BoB region. Modern palynological studies and statistical analyses of pollen percentages reveal that arboreal pollen and spores are easily transported by water in the middle and lower BoB. Peaks in their relative abundance indicate multiple wet intervals during the last glaciation.