ABSTRACT: The recent demonstration that Rubisco activity in phytoplankton is regulated in response to changes in irradiance allows development of a mechanistic model of the photosynthetic response to fluctuating irradiance. The model was used to predictphotosynthetic responses during mixing in estuarine systems, the only environments in which the rate of change of irradiance is likely to occur on time scales comparable to induction of photosynthesis. Non-steady-state rates of photosynthesis werecalculated based on the lags associated with activation and deactivation of Rubisco in response to an increase or decrease in irradiance. Non-steady-state rates were compared with steady-state rates, calculated assuming an instantaneous change inphotosynthetic response to a change in irradiance. Simulations were run for a deep, relatively clear estuary and a shallow, turbid estuary, using input parameters measured in Delaware Bay (DE, USA) and San Antonio Bay (TX, USA), respectively. Whenestimates of production are based on steady-state rates of photosynthesis, the model predicts average overestimates of 14% in the former and 22% in the latter. Sensitivity analyses show that, within the range of reported values, the model is moresensitive to changes in turbidity than to changes in the depth of the mixed layer, incident irradiance or diffusivity. When compared with published data, the model tended to overestimate the reduction in photosynthesis in the deep bay condition, possiblybecause of a compensating increase in photosynthesis due to alleviation of feedback limitation by mixing. In contrast, the model provided reasonably accurate estimates in the shallow bay condition. This suggests that while induction is unlikely to imposea constraint on production in relatively deep and clear estuaries such as Delaware Bay, it may impose a severe constraint in the shallow, turbid estuaries typified by San Antonio Bay.