During pre-pandemic time, organochlorine pesticides (OCPs) and polychlorinated biphenyls (PCBs) were investigated in the surface water of Periyar River (PR) and Bharathappuzha River (BR) in Ernakulam and Malappuram districts of Kerala, respectively and Adyar River (AR) and Cooum River (CR) in Chennai district of Tamil Nadu. After the outbreak of COVID-19 pandemic, variation in OCPs and PCBs were evaluated for AR and CR. Dominance of β-HCH and γ-HCH in south Indian rivers indicate historical use of technical HCH and ongoing use of Lindane, respectively. In > 90 % sites, p,p′-DDT/ p,p′-DDE ratio was < 1, indicating past DDT usage. However during the outbreak of the COVID-19 pandemic, elevated p,p′-DDT in AR and CR reflects localized use of DDT possibly for vector control. Similarly, during the first wave of pandemic, over a 100-fold increase in PCB−52 in these rivers of Chennai mostly via surface run-off and atmospheric deposition can be reasoned with open burning of dumped waste including added waste plastic in the solid waste stream. On contrary, a significant (p < 0.05) decline of dioxin-like PCBs level, suggests lesser combustion related activities by the formal and informal industrial sectors after the lockdown phase in Tamil Nadu. Eco-toxicological risk assessment indicated a higher risk for edible fish in PR due to endosulfan.