Mercury (Hg) bioaccumulation in fish poses severe threats to the food safety and human health. This study was conducted to assess Hg bioaccumulation in fish (n = 24) and scalp hair (n = 77) of the fishing communities at up- and downstream of the river Swat, Pakistan. The mean Hg concentration in upstream fish Salmo trutta fario (Brown trout) and Schizothorax plagiostomus (Swati fish) species was 34.7±18 μg kg−1 and 29.4±15 μg kg−1, respectively. The mean Hg concentration in downstream Swati fish, Crossocheilus diplochilus (Spena deqa), and Garra gotyla (Tora deqa) was 65±21 μg kg−1, 123±33 μg kg−1, and 326±53 μg Kg−1, respectively. The mean Hg concentration in scalp hair of the up- and downstream fishing communities was 658±125 μg kg−1 and 3969±791 μg kg−1, respectively. Independent T-test showed significant difference (p < 0.001) in the mean Hg concentration in scalp hair of the up- and downstream communities. The most prevalent health problems found in the fishing community were muscle pain, headache, visual impairment, arterial blood pressure, anemia, and kidney dysfunction. Multiple linear regression indicated that daily and weekly consumption of the fish significantly increase Hg accumulation in human scalp hair. Regular consumption of fruits and cruciferous and leafy vegetables were found to reduce Hg toxicity in the population. Further studies are recommended to identify the sources of Hg and welfare impact of fish contamination on the fishing community of river Swat.