Throughout the coronavirus (COVID-19) pandemic, the sanitizing products benzethonium chloride (BEC) and polyhexamethylene guanidine hydrochloride (PHMG-H) were widely used; however, few studies have investigated their combined toxicity to organisms. In the present study, acute toxicity and genotoxicity of BEC, PHMG-H, and the combination of the two were investigated as endpoints using Daphnia carinata as the model organism. For individual reagents, PHMG-H was found to be more toxic than BEC in terms of both mortality and genotoxicity. DNA damage and survival rate were used as toxicity endpoints. The interaction was evaluated with the concentration addition (CA) model via toxic unit (TU) approach and additive index (AI) method in mixtures at different ratios in TU. Only the binary mixture BEC + PHMG-H at the ratio 1:9 in TU was regarded as synergistic, while all others indicated increased antagonistic effects as the proportion of BEC increased over the PHMG-H concentration. The findings here benefit understanding surrounding precisely how BEC and PHMG-H interact at different mixing ratios, and can assist with the evaluation of risk assessments for binary mixtures in aquatic ecosystems.