The establishment of adequate solutions for environmental issues of a water sector in each country requires an objective database of water resources, the development, introduction and improvement of the scientific-based methods for processing of the analytical data of surface water quality. The main issue is the development of water quality assessment methods, which will include the various characteristics of a surface water and will be determined by a list of hydrochemical parameters. For this propose, the Water Quality Entropy Index (WQEI) and Armenian Water Quality Index (AWQI) were develop by us. These indexes determine the level of water pollution by a wide range of hydrochemical parameters. The AWQI characterizes the hydro-ecological system by a correlation between the order and chaos, which are measured by the geo-ecological syntropy (I) and the Shannon entropy (H), respectively. In these calculations, the pollution level of a water body can be presented as a system of the hydro-chemical parameters, which exceed the Maximum Allowable Concentration (MAC). For an example, the water quality of several rivers in Armenia was assessed by AWQI. It was shown that AWQI has a straight relationship with the other type of water quality indexes, such as the Water Quality Specific Combinatory Index and the Water Quality Canadian Index.