The multifunctional role of aquatic ecosystems on rural areas was analyzed and described in this paper. Among the most important issues this article discussed the water cycling and energy flow in aquatic ecosystems, their influence onto agricultural landscape biodiversity development and their role as biogeochemical barriers. Finally, the main principles of aquatic ecosystems protection were presented. The structure of heat balance of water ecosystems is similar to shelterbelts. Aquatic ecosystems intensify the process of evaporation and what is more, the smaller area of pond the bigger evaporation. Despite potential looses of water, it was proved that water ecosystems can be used to water (drainage) outtlow retention, and in this way they allow to increase the useful water capacity in the catchment area. Aquatic ecosystems and plants which are at the edge of them play an important role as biogeochemical barriers. They control the migration of non-point agricultural pollution. Moreover, small aquatic ecosystems of country area are mentioned to be the richest as regards the number of flora and fauna species. They influence onto biological diversity and species richness of, not only the water niche, but also the surrounding areas. That is why, they have to be protected. Among the protection guidelines, the principles of flora and fauna as well as water quality and water resources protection and renaturization of degraded ecosystems were described.