Structural and functional characteristics of communities of benthic invertebrates are a reflection of the joint influence of environmental factors (hydrological, hydrochemical and hydrobiological) on the state of aquatic ecosystems. The water and biological resources of the lower Prut and its connected water bodies are highly exploited, what determine the modification of living conditions for water inhabitants, including benthic fauna. In order to assess the current state of benthic invertebrates, there have been collected more than 40 samples during December of 2013 - August of 2014, sampling being done at seven stations: riverbed - upstream gotesti, downstream gotesti, Cahul, Slobozia Mare, giurgiulesti and lakes - Manta and Beleu.Standardized collecting and processing methods have been applied. The Petersen grab with area of capture of 1/40 m 2, a dredge with area of capture of 8 m2 and a hand net have been used for sampling. Individuals have been sorted and identified by using identification keys (Jadin, 1952; Mordukhai-Boltovsky, 1968, 1969, 1972; Kutikova, Starobogatov, 1977; Tsalolikhin, 1994, 1995, 1997, 2000, 2001, 2004). The works have been performed at the stereomicroscope SteREO discovery.v8 (Zeiss)and upright microscope axio imager А.2 (Zeiss). The highest values of abundance were registered for zoobenthos without mollusks in March of 2014 at Cahul station (7920 ind./m2)and for total zoobenthos – in July of 2014 at Slobozia Mare station (11880 ind./m2). The significant part of the abundance of zoobenthos without mollusks consisted of Tubificidae (1120 ind/m2)and Chironomidae (960 ind./m2). The abundance of total zoobenthos at Slobozia Mare station was mainly determined by mollusk Lithoglyphus naticoides – 11520 ind./m2. The lowest values of abundance were recorded in December of 2013 at Slobozia Mare station - 90 ind./m2.Surprisingly, the highest value of biomass of total zoobenthos was registered in July of 2014 at giurgiulesti station -1360.56 g/m2, of which 1360 g/m2 consisted of unio tumidus. This phenomenon occurs very rarely at given station. The lowest value of total biomass was recorded in December of 2013, as in many cases, at Giurgiulesti station - 0.08 g/m2. Altogether, there it has been collected and identified 104 invertebrate taxa, including 12 taxa of annelida, 19 - of Chironomidae, 14 - of Crustacea, 6 - of Ephemeroptera, 5 - of trichoptera, 18 - of gastropoda, 8 - of bivalvia and 22 taxa of other groups. The highest biodiversity was registered in the group of Chironomidae - 19 species. The number of species varied significantly at each sampling site – from 8 upstream to Gotesti up to 41 in Beleu lake. This difference is caused by various ecological conditions: hydromorphological, hydrochemical, type of substrate, and level of anthropogenic load. For example, at Gotesti station the substrate is formed by clay. In Beleu lake the samples were collected in the channel, which makes the link between the Prut River and lake, and directly from the lake. The investigated substrates were very different: the shells of molluscs, sand, silty sand,silt, tree roots, stands of macrophytes. It should be noted that reophylic conditions in the channel and limnophylic in the lake itself contribute to the formation of a great variety of living conditions for many species of benthic invertebrates.Beleu lake is a shallow water body, because of this one of the natural factors affecting the formation of lake benthic fauna is the high summer temperature. As example, in the outflow channel of the lake a very high water temperature was registered on 21 July 2014 – 31.2 0С. At the same time the floating dead individuals of alien bivalve species sinanodonta woodiana were observed. The cause consisted of the high temperature of the water, affecting the intensity of hydrobiont metabolism and their need for a certain content of dissolved oxygen in the water. s. woodiana demonstrates high adaptive possibilities, e.g. the capacity to penetrate into the substrate at depths in the case of unfavorable conditions, because of this it is extremely difficult to register this species in samples collected by standardized methods. Thus, on 21 July 2014 in Beleu lake was discovered only one juvenile individual of s. woodiana. The s. woodiana continues to increase its areal upstream of the Prut River – in May of 2014, downstream to gotesti, a mature individual (length – 13.5 cm, biomass – 228 g), with glochidia larvae in gills, was found in the sample collected by dredge.There has been remarked the presence of alien species at stations, where they had not been previously met. For example, Ferrissia fragilis (Tryon, 1863) was registered for the first time in Beleu lake (July of 2014), with a density of 40 ind./m2 and a biomass of 0.04 g/m2. It is important to mention that this north-American freshwater gastropod mollusk resembles morphologically with local species acroloxus lacustris, this fact making difficult its identification.acknowledgement: The study was performed in the frame of EU Joint Operational Program Romania-Ukraine-Republic of Moldova, project MIS ETC 1676