Bacteria play a crucial role in aquatic ecosystems by participating in all cycles of transformation of the main nutrients as well as in the production and destruction of autochthonous and allochthonous organic matter. The aim of this work was to evaluate the current status of microbiological regime in the lower sections of Prut river (Leova-Giurgiulesti st.) and Danube river (Galati-Vilkovo st.). Microbiological investigations were carried out during 2013-2015. A total number of 79 water samples from Prut River (Leova, Gotesti, Slobozia Mare and Giurgiulesti stations) and Danube River (Galati, Reni, Isaccea, Kiliya, Izmail and Vilkovo stations) were collected and processed. The quantitative indices of the development of total bacterioplankton (Ntot) and its saprophytic component (Nsapr) were assessed. In addition, the water quality was evaluated according to selected microbiological criteria (Regulation HP nr.890, 2013) and the index of Nsapr / Ntot (Ambrazene 2014). Samples were collected at the surface water layer (up to 0.5 m) on the water course. Determination of Ntot was performed on membrane filters "Synpor" № 6-7, and Nsapr - by inoculation on fish-agar media (RPA). It was established that Ntot in the Prut River varied within the range of 0.3- 6.5 mln cells/ml, in the lake Manta and Beleu – within 0.3-3.9 mln cells/ml and in Danuber River - within 1.2 - 11 mln cells/ml. The indices of the saprophytic microorganisms, in the Prut river varied between 0.2-38.4 thous.cells/ml, in the lakes Manta and Beleu - between 0.4- 3.9 thous.cells/ml and in the Danube river - between 2.3 -63.76 thous.cells/ml. In comparison to 1958-1959 the quantity of total bacterioplankton in Danube river was not changed essentially. At the same time there was a steady increase in the quanity of saprophytic bacteria - indicators of water purification and the amount of easily degradable organic and ammonifying substances - indicators of putrefaction process. For example, the density of saprophytes at Ismail station was increasing from 0.44–14.8 to 41.12–60.93 thous. cells/ml. As regarding the pollution level of the investigated aquatic systems, according to the microbiological criteria and the contemporary regulations on bacteriological indices - Ntot, Nsapr, Nsapr/Ntot, the level of organic pollution in Prut and Danube rivers varies from "good" to "very heavily polluted". Thus, during September-October in 2014 at st. Goteşti and Giurguleşti in Prut River the pollution level varied from "heavily polluted" to "very heavily polluted". Particulary alarming was the numeric density of saprophytes in Danube River, which reached 63.760 thous.cells/ml. Such high pollution makes sometimes difficult to apply the existing classification system on water quality. The pollution level in Danube River on investigated sectors according to total bacterioplancton (Ntot), varied from "moderately polluted" to "very heavily polluted". The only exception is the Danube sector near station Vilcova, where in October 2014 the water quality could be attributed to class "good". Considering other indicators, such as Nsapr, Nsapr/Ntot, the pollution level of Danube River during the studied period was characterised by the status of "moderately polluted”-”heavily polluted”.