The Heilong-Amur river basin (HARB) is the largest transboundary river in Asia and is primarily located in its cold region. With global warming and geopolitical cooperation strengthening between Russia and China, the hydrology change and water security risks are receiving increasing attention. This study utilized the linear regression, Mann–Kendall, and cumulative anomaly methods to analyze changes observed in the upper HARB’s streamflow and water levels over 30 years. The collation of outcomes derived from the methods mentioned above, the indicators of the hydrological alterations process, and the range of variability approach method (IHA–RVA), coupled with results gleaned from the double cumulative curve method, facilitate a thorough evaluation of the perturbations in hydrologic indicators, as well as the impacts of anthropogenic activities. The results showed that the overall hydrological regimes of both streamflow and water levels at the Luoguhe (LGH), the Shangmachang (SMC), and the Kalunshan (KLS) displayed a mild decrease from 1988 to 2017. The streamflow decreased by 58%, 42%, and 38%, and water levels decreased by 48%, 53%, and 59%, respectively, at each station after the mutations. LGH station recorded the highest decrease rate in streamflow at 8.28 × 108 m3/a, whereas the steepest rate of decline in water levels was observed at KLS station at 0.05 m/a. Despite the decreasing trend in the high pulse count of streamflow across the three stations, a slight increase in the high pulse duration of streamflow was noted at SMC and KLS. Precipitation changes were the primary driving force behind runoff alterations, contributing 62%, 84%, and 90% at LGH, SMC, and KLS, respectively, significantly higher than the contribution from anthropogenic activities (38%, 16%, and 10%, respectively). These findings also underscore the suitability of the methodologies employed in this study for application in cold regions.