Norflurazon (Nf) and fluridone (Fd) are phytoene desaturase inhibitor herbicides that are widely used for the control of grasses and invasive aquatic weeds, respectively. These herbicides enter aquatic environments where they can negatively affect non-target plant species (e.g. algae). Their toxicity towards algae may be modified by abiotic factors such as light intensity, temperature, pH and nutrients. Investigating the effect of low temperature on the toxicity of Nf and Fd is particularly important because both temperature and herbicides affect some of the same physiological process (e.g. carotenoid biosynthesis). Here we demonstrate that Nf reduced photosynthesis in the green alga Chlamydomonas reinhardtii more strongly at 15 than at 25ºC, while Fd showed stronger effects at 25 than at 15ºC. Neither herbicide significantly inhibited photosynthesis at 8ºC. Although the overall pigment content decreased with lower temperature, there was an increase in photo-protective carotenoids relative to chlorophylls at both 15 and 8ºC in the absence of herbicides. Moreover, most of the measured pigments decreased markedly in the presence of Nf and Fd at 15 and 25ºC, including β-carotene which fell to below detection limits. The fatty acid composition was modified by temperature and the level of unsaturation noticeably increased at 15 compared with 25ºC. At 8ºC, however, despite a 2.4 times decrease in fatty acid content, the unsaturation level was similar to 25ºC acclimated cells. Monounsaturated fatty acids increased concomitant with a decrease in polyunsaturated fatty acid in the 2.5 µM Nf treatment at 25ºC. Differences in the effect of Nf and Fd on photosynthesis at 15 and 25ºC can be attributed to the marked decrease in carotenoids, which play an important role in photoprotection. At 8ºC, the apparent lack of inhibitory effects compared with control cultures could be due to enhanced photoprotection and/or decreased uptake of herbicides by the alga.