The Waikato River originates in oligotrophic Lake Taupo, but becomes chemically enriched before reaching Lake Ohakuri, where phytoplankton increases dramatically. Data were collected over 2 years, including daily measurements for 1 year of N, P, Si, and chlorophyllain water leaving the lake. The hypolimnion remained stagnant in summer, and inorganic‐N peaked after lake overturn. NO3‐N showed a marked seasonal cycle in concentration and total flux in water leaving the lake, which may not correspond with input rates from the catchment.Melosira granulatavar.angustissimadominated the phytoplankton in summer, andChlamydomonasspp. andCyclotellaspp. in winter. In summer, weekly cycles in algal abundance, which correlated inversely with NO3‐N and DRP concentrations, were dictated by weekly flow cycles resulting from the requirements of hydro‐electric power generation. Flow rate and temperature appear the dominant factors regulating phytoplankton abundance. Shorter residence time and probably slower growth rates in winter, and longer residence and more rapid growth in summer interact critically. Phytoplankton production in river lakes such as Ohakuri with a brief water residence time is more appropriately represented by the mass flow of algal material through it than by the abundance of the standing stock. Summer phytoplankton biomass in Lake Ohakuri is equivalent only to a mildly eutrophic condition, but the amount generated and then lost from the lake is equivalent to production in a lake of much higher trophic status in a closed basin.