The freshwater ecosystem and its parasitic diversity are poorly addressed. Besides their pathogenicity to farmed fish, parasites are excellent ecological players and indicators. Failing good husbandry practices, including optimum stocking, nutrition, and animal welfare, fishes are invariably encountered by parasites, which opens windows for disease incidences and also results in concomitant opportunistic pathogens to establish. Furthermore, the transmissions of these parasites are strongly influenced by critical environmental parameters such as water temperature, alkalinity, and overcrowding, which necessitate and underline the importance of management and prophylaxis. Parasites cause substantial pathological debilities in the host at the cost of its energy and growth, leading to huge mortality and economic losses. The emergence of parasites is a real challenge due to significant changes induced by global warming, pollution, and shifts in aquaculture practices. Appropriate diagnosis and treatments are essential to minimize the impact of parasitic infections. In this background, this chapter provides information on parasite diversity, prevalence, and life cycle, as well as a few research thrust areas of commonly encountered parasites in freshwater aquaculture.