Artemisinin, an antimalarial compound derivated from the cultivated plant Artemisia annua L., is produced in situ through cultivation of A. annua under different climatic conditions. The bioactive compound artemisinin has been observed to spread to the surroundings as well as to leach to surface- and groundwater. To make better risk assessments of A. annua which is cultivated under varying climatic conditions, the temperature-dependent toxicity of artemisinin toward the green algae Pseudokirchneriella subcapitata and the macrophyte Lemna minor was evaluated at temperatures ranging from 10 to 30 °C. To include a possible effect of temperature on the degradation rate of artemisinin, artemisinin concentrations were measured during the experiment and toxicity was related to the time-weighted averages of exposure concentrations. The toxicity of artemisinin toward the macrophyte L. minor and the algae P. subcapitata increased with increasing growth rates, and we conclude that bioavailability plays a minor role in the observed relation between temperature and toxicity of artemisinin. The obtained results are important for possible future risk assessment of A. annua cultivation.