The paper presents historical background, up-to-date situation and future perspectives for the development of nutrient pollution threats to European surface water quality, as well as the evolution of the approach to water pollution. Utilized agricultural area in European countries is slightly diminishing, however the consumption of mineral fertilisers is steadily increasing. The consumption in Europe in the years 2015–2030 is projected to increase by 10%, and in the world by 20%. Both climate changes leading to the increase of temperature even of ca. 6°C (in comparison to the pre-industrial period) and accelerated soil erosion due to high intensity rainfall cause increased productivity of water ecosystems. Those aspects have to be taken into consideration in water management. Due to legal regulations introduced in the last twenty years, wastewater treatment has been made more effective and population connected to wastewater treatment systems has increased. The improvement has been seen mainly in eastern and southern parts of Europe. After the implementation of Water Framework Directive theories regarding modern water management have been developed, with the aim to increase the ecosystem’s capacity and its resilience to climate changes and anthropopressure.