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The source region of the Yangtze River (SRYR) is located in the Qinghai-Tibet Plateau, where the climatic conditions and alpine-cold natural conditions are harsh. Field investigations of the hydrochemical characteristics and larva and juvenile fish in rivers of the SRYR were carried out in July 2018 with the aim of obtaining further information on the unique ecological environment status of this plateau area. The results of the present research indicated that majority of the river water quality parameters in the SRYR were in the range of class I to class II, according to the classification of the environmental quality standard for surface water (GB3838-2002) in China. Among 12 kinds of metal ions, the concentrations of four major ions occurred in the following order: Ca &gt; Na &gt; Mg &gt; K. The concentrations of eight heavy metal ions (Fe, Mn, Cu, Zn, Pb, Cd, Cr and As) were all within the class I water range based on GB3838-2002. A total of three species of larval and juvenile fish, i.e., <i>Triplophysa stenura</i> (<i>T. stenura</i>), <i>Schizopygopsis microcephalus Herzenstein</i> (<i>S. microcephalus</i>) and <i>Triplophysa bleekeri</i> (<i>T. bleekeri</i>), were collected from 11 sampling sites. It was found that <i>T. stenura</i> covered the widest distribution range and was the most abundant. The results of principal component analysis and canonical correspondence analysis demonstrated that the distribution of <i>S. microcephalus</i> exhibited a positive response to water temperature, a positive response to K and a negative correlation with water temperature were demonstrated in the distribution of <i>T. stenura</i>. <i>T. bleekeri</i> distribution had a positive response to Cu, but negative responses to total phosphorus and total dissolved solid.