This study evaluates the risks of pesticides applied in rice-fish and rice farming, with and without integrated pest management (IPM) strategies, to non-target aquatic organisms in two provinces of the Mekong Delta, Vietnam. Pesticide inventories and application patterns were collected from 120 Vietnamese farmers through interviews. Risks were assessed using (1) Pesticide RIsks in the Tropics to Man, Environment, and Trade (PRIMET), a first-tier model, which calculates predicted environmental concentrations (PECs) of pesticides in the rice field, based on the compound’s physico-chemical properties and the application pattern, and then compares the PECs to safe concentrations based on literature data, and (2) species sensitivity distribution (SSD), a second-tier assessment model using species sensitivity distributions to calculate potentially affected fraction (PAF) of species based on the PECs from PRIMET. Our results show that several of the used insecticides pose a high risk to fish and arthropods and that the risks are higher among rice farmers than among rice-fish farmers. This study indicates that the PRIMET model in combination with SSDs offer suitable approaches to help farmers and plant protection staff to identify pesticides that may cause high risk to the environment and therefore should be substituted with safer alternatives.