The present study evaluated productivity under different operational (optical) conditions using the unicellular alga Nannochloropsis sp. (Eustigmatophyta). This alga is often grown in mass algal cultures because it contains high contents of the polyunsaturated fatty acid, eicosapentaenoic acid (EPA, 20:5ω3). We followed biomass, photosynthetic activities and physiological parameters in a 3 d experiment using various photosynthesis techniques in 2 outdoor cultivation systems: a flat panel photobioreactor (FPP) and a high rate algal pond (HRAP). We aimed to detect acclimation behaviour to the different optical conditions, with the FPP having a short light path and the HRAP having a long light path. Both algae cultures showed an afternoon depression of photosynthetic activity, which was more pronounced in the FPP. Therefore, the HRAP culture showed ‘classical’ shade adaptation behaviour, whereas the FPP algae was high-light acclimated. The FPP showed diurnal changes in the potential rates of photosynthesis and respiration. High temperatures (41°C) on Day 3 in the FPP caused a large reduction in the maximum Photosystem II (PSII) efficiency (Fv/Fm) and an over-reduction of the PSII acceptors, which did not recover during the light period. Chlorophyll fluorescence measurements with and without dark adaptation suggested that the decreased photosynthetic activity was due to both chronic and dynamic downregulation. Photodamage was higher in the FPP, but most was recovered during the evening. A comparison between the quantum efficiencies for PSII charge separation and oxygen evolution revealed a close coupling between the 2 processes. We also concluded that the optical absorption cross section of PSII equalled 75% of the total absorption cross section.