Abstract
The bioindication methods have been implemented for the first time for the analyses of water properties in six mineral and thermal springs of Pamir. The studied environment was characterized as flow-alkaline, well oxygenated with low salinity, and low to middle organically polluted. Studied diatom communities preferred periphytonic and benthic habitats of temperate temperature waters. Bioindicator species preferred photosynthetic way of protein synthesis. In first time assessed the trophic level of each studied source show that all they have a state from oligotrophic to mesotrophic. Bioindication methods revealed the effectiveness of nature conservation system in Tajikistan and relevance of bioindication methods using in purpose of assessment and monitoring of water sources on the protected territories.