Microplastic pollution endangers both aquatic and terrestrial ecosystems. Their spread across the food chain also endangers human health. Wastewater treatment plants (WWTPs) can be viewed as the final barrier between microplastics and the environment. In addition, it is well-known that water mites are abundant parasites in aquatic ecosystems, and nearly all insect orders with aquatic stages are considered potential hosts for at least one water mite species. However, no studies have been conducted to test the direct and indirect effects of parasites on population dynamics in freshwater ecosystems or the role of predators in shaping the behavior and life histories of aquatic organisms. Thus, this work aimed to study the seasonal abundance, distribution, composition, and risk assessment of MPs in surface water, aquatic insects (Coroxide and Notonectidae), and for the first time, water mites (Hydrachnidiae), as well as the effect of water mites’ parasitism on the number of MPs ingested by aquatic insects in two of the most polluted wastewater sites (S1 and S2) in Sohag Governorate, Egypt. The two wastewater sites receive different wastewater inputs (domestic and industrial). The results showed that the MPs abundance in surface water was higher in S2 than in S1 during the four seasons of the year, where the microplastic abundance in surface water was 2.05 ± 0.79 and 3.01 ± 0.9 particles/L in S1 and S2, respectively. Also, MPs were significantly higher in S2 in two insect taxa (Corixidae and Notonectidae) that are known to be infected by water mites. In contrast, the number of MPs was lower in S1, where water mites were absent. In addition, our results showed that adult water mites accumulated MPs. Overall, the 500–2000 µm size range was the most prevalent for both wastewater sites. Fibers were the most common MP morphotype discovered, followed by fragments. The dominant colors of MP were blue, red, and black. Furthermore, FTIR spectroscopy revealed the existence of three distinct polymers, namely polyester (PES), polypropylene (PP), and polyethylene (PE). To the best of our knowledge, this is the first study to examine the effect of water mites’ parasitism on the number of MPs ingested by aquatic organisms. However, Further research is needed to confirm our suggestion.