In aquatic environments, microplastics pose alarming threat to the environment since they actively convey hazardous contaminants and aggregate into biota. Although studies on microplastics in freshwater ecosystems have increased recently, there are still many concerns about the origins, sources, fate, and distribution of MPs. This thorough review includes 167 studies (2017–2024) with an aim to provide knowledge of the type, sources, and detection of microplastics in freshwater ecosystems, along with their consequences on aquatic species and human health. The main sources of microplastic in freshwater ecosystems include improperly disposed plastic trash, industrial raw materials, personal care items, and synthetic fabrics. Factors like retention time, flow rate, and seasonal variations influence their permanence in freshwater (FW) ecosystems, ultimately leading to their transport through river networks. The most hazardous polymers identified are PUR, PAN, PVC, Epoxy resin, and ABS. Previous studies have confirmed their ‘Trojan horse effect’ due to their ability to adorb drugs (e.g., acyclovir, atenolol, sulfamethoxazole, and ibuprofen), heavy metals (As, Cd), pesticides (difenoconazole, buprofezin, imidacloprid), antibiotic-resistant genes and microorganisms. Microplastics carrying above pollutants may possess carcinogenic properties and other health risks, considering their entry into the human body through FW-sourced water and food products. Currently, there is a lack of standardized protocols for the identification, assessment, and quantification of MPs in freshwater ecosystems. The common identification techniques are spectroscopy, Microscopy, mass spectroscopy, and novel methods like staining and AFM-IR spectroscopy. The multifaceted impact of microplastics on FW ecosystems, from contaminant transmission to human health, underscores the intricate interactions within this environmental challenge.