Ecotones, or boundary zones between land and inland waters (such as lakes, streams and rivers), are the principal routes for transport of organic matter and nutrients across landscapes via physical and biological vectors. The ecotone is the place of cumulation and transformation of in situ production as well as of allochthonous material from adjacent aquatic and terrestrial systems. The ecotype functions as an important barrier or filter for principal nutrients, such as phosphorus and nitrogen, responsible for the eutrophication and degradation of surface waters. Intensive forest cutting, agriculture, pollution and bank regulation, urbanization and hydrotechnical constructions seriously endanger the ecotone systems and damage their protective function. It is vital to develop a scientific understanding of the behaviour of phosphorus and nitrogen in these transitional boundary habitats. Such an understanding is important for the rational protection, management and restoration of ecotones connected with lakes and rivers. The importance of nutrient cycling and retention is discussed from the point of view of ecotone function, management and reconstruction in order to sustain its protective role for water bodies. Various types of land/water transitory zones are discussed: wetlands, lake littoral systems, riparian zones of rivers, streams and brooks, the contact zones between groundwater and surface waters of lakes and rivers, air--water interfaces, and patch/ecotone structures in watersheds.