1. The metabolic balance of plankton communities, commonly assessed by the photosynthesis-to-respiration ratio (P : R), has received much attention recently in connection with allochthonous organic subsidies to lakes, while the role of physical, climate-related forces has received less attention.

2.  Here we evaluated the effects of wind and upwelling events on plankton metabolism and the potential of stable oxygen isotopes to characterise P, R and P : R on the scales necessary to characterise properly physical forcing effects in large lakes.

3. We measured the ¹⁸O/¹⁶O ratio of dissolved oxygen and water in a large productive embayment of Lake Ontario (Hamilton Harbour, Canada) and estimated P, R and P : R from the steady state solutions of a widely accepted mass balance model, together with estimates of wind-driven gas exchange, and compared the results with those from experimental incubations of plankton samples.

4.  Estimates of P, but not R, from the isotope model were significantly correlated with bottle estimates while average P : R was similar by both methods. Closer examination of physical forcing events led to a model of how wind events induce mixing, upwelling, exchange and consequent changes in P and R. These physical forcing events were captured more by the isotope model than by the bottle estimates, as episodes of immediately increased R and decreased P : R, with a subsequent stimulation of P.

5. The oxygen isotope approach provided valuable measures of plankton metabolism and helped to characterise more effectively the substantial effects on P : R of physical forcing and, in particular, mixing and exchange events.