Killifish inhabit shallow freshwaters where they tolerate varied salinity regimes, resist low oxygen, and are known for their ability to control mosquito larvae populations. Environmental conditions strongly influence parasite transmission. There is a lack of studies on pathogenic killifish infections in Oman, despite their consumption by local populations. This study highlights the significance of understanding parasitic infections in killifish due to their potential impact on ecosystem health, water quality, and risks to other organisms and human health. The aim of this research is to investigate the infection prevalence of metacercariae Clinostomum in Omani killifish, Aphaniops stoliczkanus and A. kruppi, along salinity gradients and other water parameters. Furthermore, the infection intensity and incidence in relation to fish size, gender, and fish organs will be studied. Five sites were sampled using trap nets from the Al Amerat region to the mangrove area in Al Qurum. Infection prevalence decreased progressively toward the sea: 75%, 56%, 10%, 0%, and 0% at sites A through E, respectively. Water analysis revealed higher total dissolved solids and turbidity at sites A, B, C, and D. Larger killifish and females showed greater susceptibility to Clinostomum spp. infection, with the trunk region being the most commonly infected body part (36% of parasites). These findings contribute valuable baseline data for future monitoring efforts in Omani freshwater ecosystems and underscore the importance of considering environmental parameters in fish health assessments and potential biological control applications. Further research incorporating seasonal variation, intermediate host distribution, and molecular characterization of parasites would strengthen our understanding of this ecologically important host-parasite system.