Extensive research of the variability of flows under the impact of climate change has been conducted for the Upper Indus Basin (UIB). However, limited literature is available on the spatial distribution and trends of suspended sediment concentrations (SSC) in the sub-basins of UIB. This study covers the comparative assessment of flows and SSC trends measured at 13 stations in the UIB along with the variability of precipitation and temperatures possibly due to climate change for the past three decades. In the course of this period, the country’s largest reservoir, Tarbela, on the Indus River was depleted rapidly due to heavy sediment influx from the UIB. Sediment management of existing storage and future planned hydraulic structures (to tap 30,000 MW in the region) depends on the correct assessment of SSC, their variation patterns, and trends. In this study, the SSC trends are determined along with trends of discharges, precipitation, and temperatures using the non-parametric Mann–Kendall test and Sen’s slope estimator. The results reveal that the annual flows and SSC are in a balanced state for the Indus River at Besham Qila, whereas the SSC are significantly reduced ranging from 18.56%–28.20% per decade in the rivers of Gilgit at Alam Bridge, Indus at Kachura, and Brandu at Daggar. ... mehrThe SSC significantly increase ranging from 20.08%–40.72% per decade in the winter together with a significant increase of average air temperature. During summers, the SSC are decreased significantly ranging from 18.63%–27.79% per decade along with flows in the Hindukush and Western–Karakorum regions, which is partly due to the Karakorum climate anomaly, and in rainfall-dominated basins due to rainfall reduction. In Himalayan regions, the SSC are generally increased slightly during summers. These findings will be helpful for understanding the sediment trends associated with flow, precipitation, and temperature variations, and may be used for the operational management of current reservoirs and the design of several hydroelectric power plants that are planned for construction in the UIB.