The surface of the aquatic and marsh ecosystems in the Lower Prut basin is closely related to the fluctuations of the hydrological regime of the Prut and the Danube, and partly to the rainfall regime in the region and the intensity of the silting process. The expansion of the areas of pastures and forests on the basis of aquatic ones increases the abundance of birds and plants, to a lesser extent, of mammals and fish. Most bird species have a fairly broad ecological range for the main environmental drivers, but are exposed to direct threat from reduced aquatic habitats. In the presented study, we focused on species from the Red Book of the Republic of Moldova (2015), many of which are found on the lists of other international treaties. In order to reduce the negative effects of climate change on vulnerable birds, complex monitoring of environmental components (water, soil, biota, air) is necessary to launch scientifically based measures for: reconstruction of degraded habitats; the formation of ecological corridors; expanding the areas occupied by threatened species in sectors with conditions, both optimal and at extreme limits, to ensure that, depending on the evolution of the phenomena (drying/flooding, arid/cooling, clogging, deforestation, etc.), a sufficient number of individuals of threatened species will survive.