Results of two monitoring programs obtained in the free-flowing section of the Danube downstream of Vienna were used to evaluate the effects of river restoration designed to increase surface water inputs into side-arms. Functional descriptors like hydrochemical parameters and plankton react immediately to restored hydrological conditions and offer the opportunity to elucidate the hydrological control on organic processing as an important ecosystem function in fluvial landscapes. Two hydraulic parameters were estimated and linked to basic ecological properties. The level of hydrological connectivity was defined as the average annual duration (days per year) of upstream surface connection and can be used as a 'simple to estimate' parameter within the planning phase. Water age, an adapted measure of residence time based on more detailed information, allow description of the temporal development in side-arms. Greater hydrological connectivity leads to lower conductivity levels and increased nutrient concentrations due to the shift of the dominating source to river water. The contribution of river flow is indicated by higher suspended solid concentrations in side-arms than disconnected water bodies. The phytoplankton biomass shows the highest mean values at a duration of integration of 1 month a(-1) and decrease with increasing connectivity. The relationships point to a more 'main channel like' hydrochemical situation in the side-arms, with a medium level of phytoplankton biomass and increased autochthonous carbon export. No evidence of eutrophication was found due to the shift of the side-arm from an organic matter sink to a source. On a more detailed level, water age demonstrates the temporal patterns of riverine input, the development of plankton production and the shift between hydrological and biological control of phytoplankton vs. riverine flow in a side-arm. The hydrologic parameters were useful predictors for evaluating the effects of restoration measures in river floodplain systems.