We have developed a new clean-up method, which consisted of solid-phase extraction on a Sep-Pak PS-2 (styrene–divinylbenzene copolymer) or Excelpak SPE-GLF (polymethacrylate) cartridge instead of conventional ODS silica gel and silica gel together with following immunoaffinity purification using anti-microcystin-LR monoclonal antibodies. This newly developed method was demonstrated to eliminate co-existing substances and to concentrate microcystins in the lake water. The recoveries from lake water (1 liter) spiked with 100 ng each of microcystins-RR, -YR and -LR were 85.5, 89.2 and 92.2%, respectively, with coefficients of variation of 3.3–7.6%. Only 3 h were required to complete the total procedures starting from the microcystin extraction, the immunoaffinity purification, and the quantification using HPLC. The detection limits for all of the 3 microcystins in lake water were 0.005 μg/l. Applicability of this method has been demonstrated by measuring the concentrations of microcystins in water samples collected from lakes where water blooms occurred, which turned out to be 0.012–0.177 μg/l of total microcystins.