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Understanding rainfall characteristics plays a vital role in sustainable watershed development and management, but at the same time it is challenging in mountainous regions, due to its topography complexities. This study investigates the seasonal along its associated months and annual rainfall characteristics and their variations over two distinct river basins; Kaligandaki in central west and Koshi in eastern Nepal, located on the southern slopes of the central Himalayas, which is crucial to the research of the climate change in these regions. The rainfall data series over the period of 34-year (1981-2015) of 43 stations between the elevation range of 143 m asl to 3870 m asl was used for this study. The analysis was carried out to assess the significance of rainfall trend along with its magnitude followed by its abrupt shift by using the Mann-Kendall test, Sen's test and Sequential Mann-Kendall test respectively. Furthermore, multitaper method was used to confirm the influence of large-scale circulation indices over the study area. An increasing pattern of rainfall from south to north was observed throughout all season in Koshi basin which was not seen in the Kaligandaki basin, indicating the effects of orography along with monsoon. Both basins share a similar pattern of rainfall between annual and monsoonal rainfall, supporting that both basins are dominated by the monsoon. The transition months between the seasons showed almost similar spatial distribution but different from other months of respective seasons. The results showed that the seasonal and annual rainfall declined in most of the stations of both the basins, except during pre-monsoon where it showed increased rainfall. But only a few stations showing such changes were statistically significant. In fact, these noticeable significant decreases were observed especially in the southern and northern region of Koshi basin while in Kaligandaki basin, it was found either in central or in the southern region. Furthermore, the trend shift analysis identified change points during 1980s or early 1990s, but most significant shifts were observed in recent years with some exceptions. Spectral analysis showed significant peaks at periodicity ranging 2-5 years, suggesting a potential association with Quasi-Biennial Oscillations (QBO) and El Nifio-Southern Oscillation (ENSO).