Satellite-based remote sensing allows for global estimates of phytoplankton primary productivity by converting measurements of ocean color or photon absorption into units of carbon fixation. Models which perform this conversion often require an estimate of phytoplankton photoacclimation state such as the carbon to chlorophyll a ratio (C:Chl). Recently, our group developed a new photoacclimation model that can be applied to models of primary production. The model assumes that the phytoplankton photoacclimation state is not affected by periods of darkness during deep mixing beneath the photic zone, due to reduction in the plastoquinone pool in darkness and the subsequent deactivation of the signal for chlorophyll synthesis. In this study, we tested these assumptions by culturing the marine diatom Thalassiosira weissflogii under fluctuating light conditions simulating three different optical depths with progressively increasing deep mixing periods. The photoacclimation state, measured by the ratio of C:Chl, in T. weissflogii was not affected by changes in the length of simulated deep mixing periods. In addition, analysis of photosynthesis vs. irradiance (PE) curves showed that increases in optical depth caused decreases in both the maximum Chl-normalized rate of photosynthesis (Pbmax ) and in the slope of light-limited photosynthesis (αb ), but had no effect on the half-saturation irradiance (Ek , another metric of photoacclimation). However, measurements of chlorophyll fluorescence during simulated deep mixing did not support the hypothesis that the PQ pool was reduced during dark periods. Thus, our findings support the use of the photoacclimation model for estimating primary production while suggesting the need for further research into the mechanisms controlling photoacclimation in the upper mixed layer environment of the ocean.