Cover of higher plants (in 4 × 4 m plots), groundwater table height, and water chemistry in boreholes were sampled at 43 sites along three cross-sectional transects in a flat floodplain of the Upper Vltava River in the Šumava Mountains (Šumava National Park, Czech Republic). The goal was to describe the relationships between vegetation and alluvial environment. Correlations between hydrochemical and plant community characteristics were calculated, and Canonical Correspondence Analysis (CCA) was used to express relationships between the abiotic factors and vegetation. The following characteristics were significantly correlated with the vegetation pattern: mean height of the water table, distance from the river, pH, and concentration of NH4 and humic acids in the groundwater. Two distinct zones were distinguished in the floodplain: Zone I was under direct influence of the river, and exhibited higher pH and ammonium content in a fluctuating groundwater table. Zone II, covering more than half of the floodplain extent, was under the prevailing influence of water coming from the adjacent upland, and exhibited lower pH, higher content of humic acids, and a higher and relatively stable groundwater table. A diverse mosaic of the riparian communities, especially of tall-sedge and tall-grass marshes and alluvial meadows, was typical for the former zone, while peatland vegetation characterised the latter one. The floodplain exhibited a rather oligo- to mesotrophic status with only very local eutrophication, and harboured diverse and valuable plant communities. The protection of this floodplain should be among the priorities of the National Park authorities.