This study reports the baseline data of chlorination disinfection by-products such as trihalomethanes (THMs) and their associated health risks in the water distribution network of Islamabad and Rawalpindi, Pakistan. THM monitoring was carried out at 30 different sampling sites across the twin cities for 6 months. The average concentration of total trihalomethanes (TTHMs) and chloroform ranged between 575 and 595 μg/L which exceeded the permissible US (80 μg/L) and EU (100 μg/L) limits. Chloroform was one of the major contributors to the TTHMs concentration (>85%). The occurrence of THMs was found in the following order: chloroform, bromodichloromethane > dibromochloromethane > bromoform. Lifetime cancer risk assessment of THMs for both males and females was carried out using prediction models via different exposure routes (ingestion, inhalation, and dermal). Total lifetime cancer risk assessment for different exposure routes (ingestion, inhalation, and skin) was carried out. The highest cancer risk expected from THMs seems to be from the inhalation route followed by ingestion and dermal contacts. The average lifetime cancer risk for males and females was found to be 0.51 × 10−3 and 1.22 × 10−3, respectively. The expected number of cancer risks per year could reach two to three cases for each city.