Seasonal variations have great impact on water quality, waterborne diseases (WBD), and related health risks. In this study, effects of seasonal variations on physicochemical parameters like pH, temperature, electrical conductivity, dissolved oxygen (DO), waterborne bacteria (total coliform and faecal coliform) and related risks on human health were analyzed in Rawalpindi and Islamabad cities by using standard methods of chemical and microbiological analysis. Results were correlated with seasonal parameters (temperature, rainfall, etc.), and also showed that all the drinking water samples were found tasteless, colorless, and odorless. Other quality parameters were found within the recommended limits of the WHO guideline. However, significant decrease in DO level in the drinking water samples was found below the recommended level of WHO guidelines. Similarly, bacterial growth was found varied in the different months and with the changing season pattern. No growth of Legionella spp. or V. cholera was found from the analyzed samples. Health risks survey showed that residents of the study area were using different means of water sources like water filtration plants, water supply, borewells, etc. People have good perception about water quality (83%). Majority of the residents (72%) were not satisfied about the water quality in Rawalpindi city as compared to Islamabad but the same number reported no regular monitoring of water quality. About 98% were familiar with the WBD and 93% educate their children about WBD. No separate record for WBD had been found in the hospitals to correlate the data with the diseases spread in the different seasons. It is suggested to maintain the separate record for WBD to correlate with the seasons along with regular monitoring of drinking water sources and check the sewerage contamination to avoid the risk of WBD.