In 1992 a 120 km long section of the Danube river, part of the border line between Hungary and Slovakia, was diverted into a new riverbed to put into operation the Gabčikovo (Bős-Nagymaros) Hydropower Plant. To follow up the environmental changes a monitoring system in the Szigetköz region, seriously affected by the diversion of the river, was established by the Hungarian Academy of Sciences. Results of the bryological monitoring work, conducted in the river branches are presented in this article. Today, the species composition of the aquatic-riparian bryophyte vegetation living in the various sections of the Szigetköz branch-system is different from that of 1991–1992. The abundance-frequency values of aquatic species have decreased, while the proportions of mesophilous long-lived species and short-lived bryophytes have increased. The changes of water requirement spectra of bryophyte vegetation and the growing importance of certain species groups indicate that the ecological conditions became drier. Apparently, the water supply system operated from 1995 provides insufficient amount of water and is inadequate to stop (and even less so to reverse) the environmental changes that took place in the branch-systems.