The intensification of anthropic pressure and rapid climate change led to substantial changes in the structure of ichthyocenoses. The analysis of status of the populations of ‘nucleus’ species from a certain biogeographic region allows reconstructing the history of environmental conditions and highlighting the current limiting factors. Thus, within the boundaries of the Republic of Moldova, the representatives of such families as Petromyzontidae, Acipenseridae, Thymallidae, Salmonidae, Lotidae, Cottidae, etc., have practically disappeared or are sporadically met. In addition to the typical reophilic and cryophilic taxa, the populations of species characteristic for the natural marshes (e.g. Carassius gibelio, Tinca tinca, Umbra krameri, Misgurnus fossilis), which were drained and supported a massive chemicalization in the 1950s - 1980s, have been affected. The multiannual analysis of ichthyocenoses of small rivers from different areas of the Republic of Moldova demonstrated a greater diversity of species indicators of clean waters (Barbatula barbatula, species of the genera Gobio and Romanogobio, Gymnocephalus cernuus, Rhodeus amarus, Neogobius fluviatilis, Squalis cephalus, Leuciscus leuciscus, Alburnoides bipunctatus, Cottus gobio, Phoxinus phoxinus, etc.) in the north and central areas of the country. From our point of view, the higher degree of bank afforestation and the greater number of underground springs, which actively contribute to maintaining of a more favorable thermal and hydrological regime, is more important in the creation of this ichthyological picture than the lower level of pollution in these areas. The most representative species of small rivers, heavily affected by the human activity, are Carassius gibelio, Rutilus rutilus, Perccottus glenii, species of genus Cobitis, and even Perca fluviatilis, which is able to form strong and long lasting associations under these conditions. Also, there have been highlighted significant changes in the fish populations of medium and large rivers, such as Dniester and Prut, under the increasing anthropogenic threats, such as fragmentation and intense clogging of rivers, excessive development of aquatic vegetation, water pollution, illicit fishing, etc. Previously, in the structure of ichthyocenoses of these rivers, the ‘nucleus’ species were members of migratory (Huso huso, Acipenser stellatus, Acipenser gueldenstaedtii, Alosa immaculata), semimigratory (Rutilus frisii, Pelecus cultratus, Rutilus heckelii) and potamodrommous (Acipenser ruthenus, Vimba vimba, Ballerus sapa, Chondrostoma nasus, Barbus barbus, Squalius cephalus) ecological guilds, most of them being litho-psammophilous and oxyphilous. Nowadays, the dominance of ecological guilds of small and medium-sized, euryoxybiontic, eurythermic, omnivore and polyphilous species, with partial spawning and increased offspring care, occur. As a rule, the invasive (Carassius gibelio, Pseudorasbora parva, Lepomis gibbosus, Perccottus glenii), intervening (Neogobius melanostomus, Neogobius fluviatilis, Neogobius gymnotrachus, Neogobius gymnotrachororus Synotrachus, Pungitius platygaster, Gasterosteus aculeatus, Atherina boyeri, Clupeonella cultriventris), as well small and medium-sized opportunistic native species (Rhodeus amarus, Alburnus alburnus, Perca fluviatilis, Rutilus rutilus, Blicca bjoerkna, Cobitis complex) form the eudominant (D5) and dominant (D4) groups in captures from the natural aquatic ecosystems.