Lake Koronia is a hypertrophic Ramsar site in northern Greece. Water level dropped progressively from approximately 6 m in the mid-1980s to 0·8 m in 2001 associated with over extraction of groundwater for agriculture, and the open water area has decreased from 4620 to 2930 ha, respectively. The resulting annual water level loss of 0·25–0·30 m year−1 was accompanied by expansion of Phragmites australis from a littoral fringe to dominance of exposed lake bottom areas from 97 ha in 1977 to 785 ha in 2005. The aim of this work was to apply an ecohydrological approach using remote sensing and geographic information system (GIS) to examine the movement of Phragmites relative to the water level retreat and to basin morphometry. Aerial expansion of Phragmites averaged 11–32 ha year−1 during the period of progressive water level decline but increased to 38–116 ha year−1 during a brief period of water level increase (2001–2003) as the plant colonized reflooded portions of the basin. The total area of Phragmites expanded 29% per annum during 1977–2005. Landward and lakeward margins of the Phragmites area followed water level retreat, moving 55 and 129 m, respectively, during the long period of progressive water level decline. Aerial movements of Phragmites in Lake Koronia are some of the highest reported in the literature. Mean water level within the Phragmites bed varied from 0·5 to 2·0 m during the period covered by this study. Very minor changes in basin slope, however, affected plant colonization rates, as evidenced by 200–250 ha/0·5 m water level drop at 0·18% basin slope to 360–1360 ha/0·5 m water level drop at 0·029% slope. The techniques applied to Lake Koronia for reconstructing past lake levels and associated distributions of Phragmites have broad application for understanding the dynamics of Phragmites elsewhere and anticipating periods of rapid plant expansion related to subtle changes in basin morphology. This study is useful for managing Phragmites populations in areas where efforts are being made to re-establish populations as well as where elimination of invasive populations is sought. Copyright © 2013 John Wiley & Sons, Ltd.