We measured changes in hydrodynamics and phosphorus cycling due to a typhoon in two morphologically distinct basins of Lake Biwa, Japan. The typhoon, with wind speeds up to 20 m s(-1), led to physical, chemical, and physiological responses that differed dramatically in the shallow (mean depth of 3.5 m), eutrophic south basin compared to the deep (mean depth of 45.5 m), oligo-mesotrophic north basin. prior to the typhoon, PO4-P concentrations were <1 mu g liter(-1) in both basins. A suite of physiological tests (protein:carbohydrate ratio, sestonic C:N:P ratios, nutrient-enrichment bioassays, alkaline phosphatase activity, P-32 uptake) all indicated that the plankton was P-deficient. Bacteria dominated (avg of 65%) the uptake of (PO43-)-P-32. As a result of the typhoon, P concentrations increased to similar to 2.5 mu g liter(-1) and suspended solids increased from 4.5 to similar to 17 mg liter(-1) in the south basin. The day after the typhoon, all physiological tests indicated that the south basin plankton was P-sufficient and that phytoplankton dominated (65%) P-32-uptake. A week after the typhoon, P concentrations had dropped to near pre-typhoon levels and the physiological tests indicated that the plankton was again P-deficient. Only on the day of the typhoon were wave-induced shear stresses great enough to cause considerable entrainment of sediment and associated pore waters in the South Basin. Because interstitial porewater P concentrations were greater than or equal to 2 orders of magnitude greater than the overlying water concentration, we concluded that the increase in P was caused by entrainment of nutrient-rich pore water. In the north basin the typhoon-induced upwelling and mixing in the thermocline did not penetrate to depths where P concentrations were elevated. Consequently, plankton were as P-deficient immediately after the typhoon as they were prior to it.