Aquatic habitats exert some unique selective pressures on parasites, from the properties of water as a medium to the fragmented nature of freshwater bodies dispersed across a terrestrial landscape. We first discuss some of the key features of aquatic habitats that may impact parasite evolution. We then summarise what is known of microevolutionary processes affecting aquatic parasites, from the forces maintaining the genetic structuring of parasite populations to the emergence of local adaptation and cryptic species. Next, we discuss host–parasite macroevolution and how different historical events have shaped patterns of host specificity. Finally, we address the impact of anthropogenic changes to aquatic habitats on current and future parasite evolution, with a focus on global climate change, fisheries and aquaculture.