This research study focused on the primary freshwater surface sources of Khyber Pakhtunkhwa (KP) province, Pakistan—Swat and Kabul rivers. The study aimed to assess microplastic (MP) contamination of fish in the Swat and Kabul rivers. Understanding this contamination is vital for evaluating the environmental and health risks associated with consuming contaminated fish and contributing to the ongoing conservation efforts. The study’s objective was to investigate the presence of MPs in the gastrointestinal tracts (GIT) of fish and to delineate the identified MP types. Samples of local dominant fish (Schizothorax plagiostomus [Swatay] and Racoma labiata [Chunr], Cyprinus carpio [Common Carp], and Clupisoma naziri [Sher Mayai]) were collected, and their body weight and length assessed to gauge the overall health. The GIT samples were processed, digested and filtered before microscopic examination to detect MPs. Subsequently, the identified MPs were subjected to attenuated total reflectance–Fourier transform infrared spectroscopy for characterization by analyzing their absorption bands. Results of the study showed the presence of MPs in fish samples, predominantly identified as polyethylene (PE), with polypropylene (PP) being the subsequently prevalent plastic type, which manifested fish contamination with MPs. The study revealed MP pollution in both Swat and Kabul rivers, with fish ingesting these particles. This poses potential health risks for fish and health of the ecosystem.