Freshwater turtles comprise 81% of all chelonian species despite freshwater systems only occupying 1% of the earth’s surface, and they are commonly exploited as pets and food resources. This contact between humans and turtles may put both sides at risk of disease transmission. Additionally, human impact on ecosystems can cause disease outbreaks in turtle populations. In this review, we focused on disease agents affecting freshwater turtles, intending to contribute to conservation and public health efforts. We analysed 423 articles and noted a post-SARS-COVID-19 peak, with most research originating from Asia, North America, and Europe. Emydidae was the most frequently studied family, and there was also a bias towards adults, live specimens, and native species. Since most of the studied turtles were wild-caught, we recommend that captive turtles should also be thoroughly studied since they can transmit diseases to other turtles and humans. We registered 2104 potential disease-causing agents, with Platyhelminthes dominating within Animalia, while Proteobacteria dominated bacterial agents. Viruses’ representation was low, highlighting gaps in reptile virology. Fungi, Chromista, and Protozoa were also underrepresented, but this is changing with the development of molecular tools. This synthesis serves as a foundation for targeted health assessments, conservation strategies, and future research, essential to mitigate ecosystem and public health threats.