This study investigated whether the toxicity of boron to the green algal species Chlamydomonas reinhardtii, Chlorella sorokiniana, and Chlorella vulgaris was affected by the presence of ethylenediaminetetraacetic acid (EDTA). As EDTA exists widely in aquatic ecosystems, its effects must be considered when assessing metal toxicity. C. vulgaris was found to be the most insensitive among the three algae, as there was little change in the toxicity of boron for this species in the presence of EDTA when compared with that for the other species. In contrast, C. reinhardtii and C. sorokiniana were both highly sensitive to boron in the presence of EDTA. Based on Visual MINTEQ modeling results, we found that EDTA combined with micronutrients. This chelation reduced their availability for uptake by the algae; consequently, the algae were highly sensitive to boron. These results will be useful for future assessments of risk and management of boron in aquatic ecosystems.