The fish health status and parasitic infection in paddy fields are understudied in Borneo. This study was done to compare the prevalence and abundance of parasites on freshwater fishes in the upstream and downstream rivers of paddy fields. Parasite study on freshwater fishes was done by collecting live fish samples using ten minnow traps with baits at each site in Serian and Padawan, Sarawak, from October 2017 until March 2018. A total of 120 freshwater fishes were examined during this study period. Cold anaesthesia was applied on live samples prior to ectoparasite and endoparasite microscopic screening, which involved scraping of outer body mucous and removal of fish intestines, respectively. No ectoparasites were recovered from the fish samples. A total of 19 (15.83%) fishes from Cyprinids were infected with endoparasites. From these, 58 individuals of endoparasites were recovered. Two groups of parasites, namely Nematoda (Cucullanus sp.) and Trematoda (unidentified), were recovered from the fish intestines. From this study, there was a significant difference between the upstream fishes and downstream fishes in their endoparasite infection at both Triboh Village (p = 0.035) and Annah Rais Village (p = 1.445 × 10-6) using two samples t-test. The endoparasite abundance in fish was higher in the streams where there was less human disturbance. This study may serve as a baseline study on the parasitic infections of freshwater fishes in streams near paddy fields or other agricultural area in Sarawak.