1. Side-arms connected to the main stem of the river are key areas for biogeochemical cycling in fluvial landscapes, exhibiting high rates of carbon processing. 2. This work focused on quantifying autochthonous and allochthonous carbon pools and, thereby, on comparing transport and transformation processes in a restored side-arm system of the River Danube (Regelsbrunn). We established a carbon budget and quantified carbon processing from March to September 2003. In addition, data from previous studies during 1997 to 1999 were assessed. 3. Gross primary production (GPP) and community respiration were estimated by diel oxygen time curves and an oxygen mass balance. Plankton primary production was determined to estimate its contribution to GPP under different hydrological conditions. 4. Based on the degree of connectivity, three hydrological phases were differentiated. Most of the organic matter, dominated by allochthonous carbon, was transported in the main channel and through the side-arm during floods, while at intermediate and low flows (and thus connectivity), transformation processes became more important and autochthonous carbon dominated the carbon pool. The side-arm system functioned as a sink for particulate matter [total suspended solids and particulate organic carbon (POC)] and a source of dissolved organic carbon (DOC) and chlorophyll-a. 5. Autochthonous primary production of 4.2 t C day )1 in the side-arm was equivalent to about 20% of the allochthonous inputs of 20 t C day )1 (POC and DOC) entering the area at mean flow (1% of the discharge of the main channel). Pelagic photosynthesis was generally high at mean flow (1.3-3.8 g C m )2 day )1 ), and contributed up to 90% of system productivity. During long stagnant periods at low discharge, the side-arm was controlled by biological processes and a shift from planktonic to benthic activity occurred (benthic primary production of 0.4-14 g C m )2 day )1 ). 6. The transformation of the organic matter that passes through the side-arm under different hydrological conditions, points to the importance of these subsystems in contributing autochthonous carbon to the food web of the main channel.

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The study was carried out during four years that span a gradient in hydrological connectivity between the Danube and its sidearm system at Regelsbrunn (Austria). We evaluated the influences of distinct periods of hydrological connectivity on the phytoplankton community structure itself, but also interferences with biotic processes (including community succession, competition and zooplankton grazing) that may take place within the constraints set by the hydrological disturbance regime. Algal biomass was highly related to the hydrological regime: lowest amounts were detected either during flood events or at long-lasting periods of isolation; on the other hand intermediate connection led to maximum concentrations. During floods and throughout the cold season, Bacillariophyceae were dominating the algal community. Summer and elongated periods of isolation favoured Chlorophyta. Cryptophyta occurred in early autumn after two months disconnection from the main channel, Dinophyta and Cyanoprokaryota were only of minor importance. Multivariate statistical analyses showed that water age was the primary determinant of phytoplankton community structure in the side-arm system. Cluster analyses revealed 7 groups that were characterized by 169 indicator taxa. Groups were dominated by Bacillariophyceae (Nitzschia, Navicula, Cymbella, Fragilaria and Diatoma), while species belonging to the Chloro-, Eugleno-and Dinophyta were less abundant. Non-metric Multidimensional Scaling was used for a comparison of community similarity between the main channel and the side-arm system. During high connectivity temporal trends of phytoplankton similarity in the side-arm tracked closely the community patterns of the Danube which indicated a major influence of the main channel on phytoplankton community structure. During low connectivity the temporal trends of the communities from both sampling stations were less coupled. A Canonical Correspondence Analysis explained 89.7% of the variance of the species-environment relation. Water age, particulate inorganic matter and dissolved inorganic nitrogen compounds were strongly coinciding with the first axis, whereas particulate nitrogen was mainly related to the second axis. A phytoplankton succession model was developed for the side-arm system. This model emphasizes increased phytoplankton community similarity during high connectivity and short isolation periods and a site-specific community development during low connectivity between the Danube and the side-arm. During prolonged isolation, seasonality gained importance in structuring the plankton community. Biotic interaction (intraguild competition and zooplankton grazing) played an important role in the shifts between successional stages, suggesting that these effects should not be neglected in ecological studies of disturbance-dependent floodplain ecosystems.