Climate changes of the last couple of decades have great impact on the plant and animal world and all habitat types on Earth. In addition, anthropogenic impacts are increasingly putting pressure on the environment due to the growing human population and the more intensive use of land and waterways. An increasing number of watercourses can’t withstand such pressure, which leads to changes in water quality and flow regime. Watercourses begin to dry up in the dry part of the year and that period lasts longer, while re-flooding of riverbeds often has fatal consequences for the surrounding population and the landscape. In order to prevent any unwanted consequences of such events on people and the environment, we need to know the hydrology and ecology of intermittent watercourses. Because of these changes, benthic invertebrate communities (as well as all the other organisms) which inhabit these watercourses have been endangered. Their variety and abudance decrease as the dry season is extended and water pollution is increased by organic matter, artificial fertilizers and pesticides. Although these communities have developed a series of evolutionary adaptations to such a demanding habitat, these are often no longer sufficient to survive and maintain diversity and abudance at a constant level. By linking scientific knowledge about hydrology of watercourses and ecology with the structure of communities that inhabit them, we will have an excellent foundation for changing legal frameworks and protecting all sources of drinking water as well as intermittent watercourses.