Around 57.1% of microsporidia occupy aquatic environments, excluding a further 25.7% that utilise both terrestrial and aquatic systems. The aquatic microsporidia therefore compose the most diverse elements of the Microsporidia phylum, boasting unique structural features, variable transmission pathways, and significant ecological influence. From deep oceans to tropical rivers, these parasites are present in most aquatic environments and have been shown to infect hosts from across the Protozoa and Animalia. The consequences of infection range from mortality to intricate behavioural change, and their presence in aquatic communities often alters the overall functioning of the ecosystem.In this chapter, we explore aquatic microsporidian diversity from the perspective of aquatic animal health. Examples of microsporidian parasitism of importance to an aquacultural ('One Health') context and ecosystem context are focussed upon. These include infection of commercially important penaeid shrimp by Enterocytozoon hepatopenaei and interesting hyperparasitic microsporidians of wild host groups.Out of ~1500 suggested microsporidian species, 202 have been adequately taxonomically described using a combination of ultrastructural and genetic techniques from aquatic and semi-aquatic hosts. These species are our primary focus, and we suggest that the remaining diversity have additional genetic or morphological data collected to formalise their underlying systematics.