The widespread occurrence of emerging contaminants (ECs) and pathogens in potable water sources has led to the need of an efficient alternative method for water treatment. Three pharmaceuticals and two pesticides were selected for the ECs degradation study in a continuous flow pulse corona discharge reactor. For a power dissipation of 58.67 W, ECs were completely removed from lake water with a flow rate of 10 mL/min. Whereas, 91–100% ECs degradation was achieved in river water after a hydraulic retention time (HRT) of 24 min. Initial bacterial concentrations were determined in lake and river water samples and subsequently, disinfection studies were carried out. With the same power input, complete disinfection (3 log reduction in river water) was achieved within HRT of 10 min. The toxicities of the ECs were completely eliminated after the plasma treatment. Several other water quality parameters were also monitored and an increase in nitrate concentration and decrease in pH value was observed after treatment. The problem of increased nitrate concentrations in the plasma treated water was tackled, thus making the plasma treated water suitable for drinking purpose. Using oxygen as a feed gas instead of atmospheric air, nitrate concentration was brought down significantly. Energy efficiency of the reactor was also compared in terms of electrical energy per order (EEO) and G value. Depending on the nature of the ECs, the EEO values ranged between 20 and 86 kWh/m3 and G-value between 8.4 and 36.8 mg/kWh in different potable water sources. The operating cost for treating ECs from contaminated water was found to be as low as 4.3 $/m3. © 2018 Elsevier B.V.