IH has a long-term experience with a study of hydrological processes in a small catchment scale – the fundamental research of the hydrologic cycle in Volyňka catchment (Southern Bohemia, Czech Republic) was established by IH in the Framework of IHD and since 1975 the continuous hydrological monitoring of the Liz experimental catchment (http://ne-friend.bafg.de/servlet/is/17796/) has been keeping on. It was necessary to supplement this monitoring by the soil hydrology and geochemical monitoring and extend them to further two headwater regions of the Czech Republic. This monitoring system is fully automatic with a wireless data transfer. At present, complex hydrological, soil-hydrological and geochemical monitoring is operated in the experimental catchments Liz in the Landscape Protected Area in the Šumava Mts. (0.99km2) and Modrý potok in the National Park of the Giant Mts. (2.62 km2). Further, three locations situated in the National Park of the Šumava Mts. differing in the vegetative cover are monitored. In order to quantify the amount of water and pollutants incoming to the ecosystems by the deposition from wind driven low clouds and fogs, monitoring systems were created in the Šumava Mts., Jizerské hory Mts, and Giant Mts. A great attention is paid to the detailed monitoring of the potential and amount of water in the vadose zone of the soil profile. For the purposes of the application of the water balance method at the forest floor and for the assessment of the interception of the forest canopy the automatic systems for parallel monitoring of the open air precipitation and throughfall were established in the Šumava Mts., Jizerské hory Mts. and Giant Mts. The original early warning system for flash floods based on new findings on the gravitationally destabilized outflow from the soil profile has been created and operated in the mountainous region of the Giant Mts. (Úpa river).