Abstract: This paper dealt with the influence of salinity and Cu2+concentration on the phytoplankton by inducing artificially the changes of salinity and Cu2+concentration of lake water. By means of experimental analysis, it found that increasing the Cu2+ concentration of lake water inhibited the algal growth, it was good for improving water quality; however, high Cu2+concentration was harmful to human health and crop growth. On other hand, as the salinity was low in Jordan river, increasing appropriately the Cu2+concentration enhanced algal growth rate in river water. The annual mean biomass of phytoplankton have showed progressively increase with salinity decreasing successively. Especially, when the salinity of lake water was low than 200μg/L, the ratio of Blue-green algae/phytoplankton caused a shift, it was harmful to water quality in Lake Kinneret. It indicate that controlling Cu2+concentration and keeping salinity is very important for the preservation of water quality in Lake Kinneret.