The unicellular alga Nannochloropsis sp. (Eustigmatophyta) is a rich source of lipids, polyunsaturated fatty acids (such as eicosapentaenoic acid) and carotenoids (violaxanthin), which makes it valuable for human consumption, aquaculture and biofuel production. Mass production of Nannochloropsis sp. can be easily achieved in high-rate algal ponds (HRAP), in flat panel photobioreactors (FPP) or in tubular photobioreactors. While easy to operate, these systems are prone to unfavorable growth conditions, which affect productivity. In the present study, we cultivated Nannochloropsis sp. in 2 outdoor production systems and monitored photosynthetic activity. Unfavorable conditions (stressors), such as high temperature and high pH in combination with high irradiance, were induced in FPP, causing a substantial reduction in the photosynthetic rate. The measurements of Nannochloropsis sp. photosynthetic activity using several chlorophyll fluorescence techniques as well as oxygen production measurements showed that this species is able to withstand high irradiance levels. Although some photodamage due to high irradiance was found, the cultures rapidly recovered. Nannochloropsis sp. coped well with high pH conditions under physiological temperatures. However, a temperature rise above 32°C was detrimental, with repair processes being unable to keep up with the rate of damage. The cultures in the FPP were more prone to damage by extreme temperatures than those in the HRAP due to the high surface:volume ratio, which complicated temperature regulation within the physiological range.