Background The presence of plastic particles in freshwater species is becoming a global concern owing to the potential impact on food security and human health. In this study, we investigated the presence microplastics (MPs) in two economically important freshwater species: the giant freshwater prawn (Macrobrachium rosenbergii) and the white leg shrimp (Litopenaeus vannamei) cultured in a polyculture pond in the central part of Thailand. Methods The gastrointestinal tract (GT) of 300 giant freshwater prawn (160 female and 140 male) and 150 white leg shrimp specimens were investigated for the presence of MPs. Results From the pooled samples, a total of 1,166 MP items were identified. Specifically, the GTs of female and male freshwater prawns and white leg shrimps contained an average of 33.31 ± 19.42, 33.43 ± 19.07, and 11.00 ± 4.60 MP items per individual, respectively. Further, their mean MP contents per g of gut material were 32.66 ± 5.10, 32.14 ± 4.85, and 10.28 ± 1.19 MP items, respectively. In the GT of these species, MPs with sizes in the range 500–1000 µm, were predominant, and white/transparent MPs were most prevalent (63.67%). Furthermore, regarding the morphotypes of the MPs, fibers, fragments, films, and spheres were frequently observed, with fibers shows predominance. Specifically, the proportions of fibers in the GTs of female Macrobrachium rosenbergii, male Macrobrachium rosenbergii, and Litopenaeus vannamei were 83.3, 79.91, and 46.06%, respectively. Four MP polymer types, polyethylene, polycaprolactone, polyvinyl alcohol, and acrylonitrile butadiene styrene, were also identified via FTIR spectroscopy, which further confirmed the presence of MPs in the GT of the freshwater-cultured species. Discussion Our findings indicated that consuming shrimps and prawns without first removing the MPs from their GTs is one of the mean by which humans get exposed to MPs. Thus, MPs in freshwater species can be passed down the food chain to humans.