Effects of high water levels on the abundance of colony-forming units of eutrophic and oligotrophic bacteria were investigated. Changes in their proportion were exploited as the biological indicator of organic substrate availability. It was also reconsidered, to a certain extent, which source (autochtonous or allochtonous) of organic substrate and bacteria prevails during floods. Water samples were collected from the surface and from the bottom during high water levels in the floodplain lake (Kopacko Lake) and the connecting channel (Hulovo Channel). The relative abundance of oligotrophs vs. eutrophs was considerably higher at the end of investigation, to which higher abundance of eutrophs preceded at Kopacko Lake sampling station. Also in Kopacko Lake, a considerably higher abundance of bacteria was noticed in the bottom samples during first intensive flooding pulses. Elevated bacterial abundance was connected with the sufficiently intensive floods (eutrophs dominate) but also with the water properties established following the settling down of disturbed conditions (oligotrophs dominate). Greater abundance in the bottom samples established during the first intensive pulse suggests a sediment origin of bacteria, while considerable differentiation between oligotrophic and eutrophic bacteria suggests an establishment of lower quality of organic substrate at the end of the investigation.