Moringa oleifera seeds are used globally as a treatment for water and contain the lectins cMoL and WSMoL, which display coagulant activity. In this study, we sought to determine the cytotoxicity and genotoxicity of the M. oleifera seed extract (SE), prepared with the same procedure that people use for treating water, as well as cMoL and WSMoL, in human peripheral blood mononuclear cells (PBMCs). Cell viability was assessed using the 3-(4,5-dimethylthiazol-2-yl)2,5-diphenyltetrazolium bromide (MTT) assay, while genotoxicity was evaluated using the comet assay, with cell nucleoids categorized in classes ranging from 0 (without damage) to 4 (maximum damage). The PBMCs treated with SE, cMoL, and WSMoL displayed viability higher than 60% in treatments with concentrations up to 100 µg/mL. In addition, SE and cMoL displayed low genotoxicity owing to the detection of nucleoids in class 1. However, the number of nucleoids in all classes increased when 50 and 100 µg/mL of WSMoL was administered, reaching a damage frequency of 50.0%. Although M. oleifera SE, cMoL, and WSMoL were not cytotoxic to PBMCs after 24 h of exposure, dose-dependent genotoxic effects were observed, especially with WSMoL. These findings indicate that caution must be exercised when selecting a lectin/extract concentration for water treatment.