This dataset documents seasonal heavy metal bioaccumulation in two commercially important edible freshwater fish species, Labeo rohita (Rohu) and Cirrhinus mrigala (Mrigal carp), collected from Head Panjnad, Punjab, Pakistan (29.3464 °N, 71.0197 °E), during summer and winter seasons of 2022. Head Panjnad represents the confluence zone of the major Punjab rivers and forms an important hydrological transition between the upper and lower Indus Basin. Fish specimens were collected from multiple locations near the Panjnad headworks, and concentrations of lead (Pb), nickel (Ni), and cadmium (Cd) were quantified in liver, gill, and muscle tissues using acid digestion followed by Atomic Absorption Spectrometry (AAS). Metal concentrations are reported as mean ± standard deviation on a wet weight basis (mg/kg ww). Across both species and seasons, bioaccumulation followed the order liver > gill > muscle, while metal abundance followed the pattern Pb > Ni > Cd. Seasonal comparisons demonstrated higher concentrations during summer relative to winter. The dataset additionally includes human health risk assessment metrics based on fish muscle consumption, including intake exposure (Exp_in), Target Hazard Quotient (THQ), Total Target Hazard Quotient (TTHQ), and Carcinogenic Risk (CR), calculated using USEPA methodologies. TTHQ values exceeded unity for both species, indicating potential cumulative non-carcinogenic concern for regular consumers, whereas individual carcinogenic risk values remained within acceptable USEPA thresholds. The dataset provides structured environmental monitoring information relevant to aquatic ecotoxicology, freshwater contamination assessment, food safety evaluation, and long-term Indus Basin biomonitoring applications.