The list of species of water invertebrates and the amphibiotic insects is analysed by results of the long-term researches in 2006 – 2015. Effects of climate transformation and change of the hydrological treatment on a condition of water ecosystems and population of such species are shown. The key factors causing negative consequences for ecosystems of the rivers, floodplain lakes and temporary waterbodies serving as biotopes of rare and endangered species of hydrobionts are defined.