The Swat and Kabul Rivers of Northern Pakistan are within an important regional watershed that support river‐based livelihoods and are impacted by untreated effluent discharges and municipal solid waste. Anecdotal evidence indicates that fish populations are decreasing in these rivers. One potential cause of poor aquatic health is pollution; therefore, we investigated the presence of Contaminants of Emerging Concern (CECs) in the river systems. Water samples were collected in the Kabul River (n=9) and Swat River (n=10) during high (summer 2018) and low (winter 2019) river flow seasons. Agrochemicals, pharmaceuticals, plasticizers, chemicals in personal care products, and hormones were quantified via liquid chromatography high resolution mass spectrometry. In the Swat River, caffeine (18 ng/L to 8452 ng/L), DEET (16 ng/L to 56 ng/L), and plasticizers (13 ng/L to 7379 ng/L) were detected at all sites during both seasons, while butachlor (16 ng/L to 98 ng/L) was detected only during high flow. In the Kabul River, caffeine (12 ng/L to 2081 ng/L) and several plasticizers (91 ng/L to 722 ng/L) were detected at all sites during both seasons, while DEET (up to 97 ng/L) was detected only during high flow. Pharmaceuticals (analgesics and nonsteroidal anti‐inflammatory drugs) were quantified in both rivers (up to 823 ng/L) with detection frequencies from 70‐100% and 0‐78%, respectively during low flow. Intermittent‐use and natural seasonal processes (increased runoff and dilution from rainfall and snowmelt) yielded higher agrochemical concentrations and lower concentrations of continuous‐use compounds (e.g., caffeine) during high flow. This study provides the first insight into CEC concentrations in the Swat River, additional insight into the Kabul River stressors, and overall, contaminant risks to aquatic life.