A floating-leaved macrophyte, water chestnut (Trapa japonica) forms dense beds covering a large part of the surface of Lake Mikata (Fukui, Japan) in summer months. We studied how seasonal dynamics of physicochemical environment and animal assemblages (macroinvertebrates and zooplankton) respond to the Trapa beds in this lake. Inside the Trapa beds, dissolved oxygen concentration decreased near the lake bottom from early summer and hypoxic environment (<1 mg-O₂ l^-1) was formed in mid-summer, although such hypoxic condition recovered as Trapa beds disappeared in late autumn. When the Trapa beds were formed in summer, chironomid larvae and oligochaetes were very scarce inside the Trapa beds whereas nematode, cladocera and ostracods were abundant. After the Trapa beds disappeared, the animal assemblages were similar all over the lake: chironomid larvae and oligochaetes were abundant but nematode and zooplankton species decreased their density. The salinity gradient also influenced the animal assemblages. Our results showed that the phenology of Trapa strikingly influenced the seasonal dynamics of the lake ecosystem, which needs to be taken into account for the ecosystem management of the lake.