The braided hydrosystem of the Szigetköz floodplain played a prominent part in the structure of the fish communities in the upper section of the middle river Danube Regulations and flood control measures have modified the natural resources of the area since the 19thcentury. At the end of 1992, the River Danube was diverted to the by‐pass canal of the Gabcikovo Hydroelectric Power Plant and most of the small tributaries to the river became dry in the floodplain. The juvenile fish assemblages have been monitored since the completion of the Dam of the River Gabcikovo. The monitoring results of parapotamic and plesiopotamic backwaters demonstrate the importance of hydrological connectivity of the floodplain tributaries.