Water scarcity is becoming a global problem especially in the arid and semi-arid climates. Besides shrinking in quantity, surface and ground waters are getting polluted due to anthropogenic activities. Management of water resources requires analysis of long-term water quality data. The present work is the first study that uses long-term data (2004-2020) of 30 water quality variables from 24 locations across rivers Satluj and Beas, the two main tributaries of river Indus flowing through India. Exploratory analysis revealed least variation in pH and dissolved oxygen (DO) and greatest variation in total coliform (T. Coli) and fecal coliform (F. Coli). Beas had 78% samples of designated best use category B (outdoor bathing), 18% of C (drinking after conventional treatment and disinfection) and 4% of A (drinking without conventional treatment but after disinfection). On the contrary, 31% samples of Satluj belonged to B, 32% to C and rest to D (wild life and fisheries) and E (other uses). Locations Mukerian (Beas) and D/S Buddha Nullah (Satluj) were identified as hot spots. Mann-Kendall analysis showed significant increasing trend for pH, chemical oxygen demand (COD), biological oxygen demand (BOD), potassium, DO, T. Coli, F. Coli and nitrite at majority of the locations. Significant decreasing trends were observed for electrical conductivity, calcium, phosphate, sulfate, total dissolved solids, chloride, nitrate and total hardness. Rising levels of BOD, COD, T. Coli and F. Coli had carryover impact on confluence waters. Therefore future remedial actions must focus on hot spots and variables showing significant increasing trends.