The limnological knowledge of waters in arid regions, especially Mongolia, is still insufficient. It was the goal of the Mongolian-German research project “Limnological Particularities of Characteristic Waterbodies in the Uvs Nuur Basin” to develop a systematic inventory of waters, describe their morphological, hydrophysical, chemical and biological characteristics and to generalize the framework of abiotic and biotic factors that determine their character. During the field work, carried out from 1996 to 1999, samples of water, sediments, benthic and planktonic biota were taken from 76 places at 15 stagnant water bodies, 21 streams and several groundwater bodies; morphological, hydrological, physical and hydrochemical measurements were made. Chemical and biological analyses were carried out in Germany. The most important taxonomical groups were determined by German and international specialists. The results of the work are presented and discussed separately for running waters, lakes and groundwater. Based on these findings, several general topics are dealt with: factors shaping the character of water bodies, food webs, biogeography, spatial sequence of water bodies, typology and protection issues. A checklist of 596 taxa was compiled; 109 additional taxa from the Russian and Mongolian literature were included. Two species (Cyclops glacialis Flößner 2001 and Acanthocorbis mongolica Paul 2011) were new for the science and 103 species were new reports for Mongolia. A regional stream typology with 11 different types was developed using the criteria ecoregion, altitude and catchment area. The typology developed for stagnant waters comprises 9 types based on altitude, lake area, existence of an outflow and relative depth. This dissertation comprises 139 pages and an appendix of 59 pages, 50 tables, 94 figures and a map.