The fluctuations of drift diatom assemblage and water quality in the lower reaches of the Nagara river part of a river system without large reservoirs, were surveyed monthly from March 1990 to February 1991. In August 1990, large planktonic diatom standing crops were recorded near the river mouth. Dominant species were Cyclotella atomus and C. meneghiniana (Bacillariophyta: Centrales). Judging from the patterns of algal distribution in the stream and of diurnal fluctuation of both flora and the standing crops associated with tidal movement, the major portion of diatom assemblage is considered to be autochthonous potamoplankton which reproduce in the main stream.Current velocity was an important controlling factor in flora and standing crops of potamoplanktonic diatoms. Maximal standing crops were recorded when precipitation in the catchment was low. After considerable precipitation, the relative abundance of exfoliated periphytic diatoms and pheo-pigment content increased.In August, when the chlorophyll a concentration increased to a peak value of 32.6 μg⋅l-1, BOD reached the maximum, 3.9 mg⋅l-1 at the lower reaches of the river, and both inorganic nitrogen and phosphorus registered lower values than in the upper stream.