The effect of a terrestrial humic acid (HA) and Suwannee River HA on the cytotoxicity of engineered zinc oxide nanoparticles (ZnONPs) and titanium dioxide nanoparticles (TiO2NPs) to natural aquatic bacterial assemblages was measured with spread plate counting. The effect of HA (10 and 40 ppm) on the cytotoxicity of ZnONPs and TiO2NPs was tested factorially in the presence and absence of natural sunlight (light irradiation (LI)). The experiment was of full factorial, completely randomized design and the results were analyzed using the General Linear Model in SAS analytical software. The method of least squares means was used to separate the means or combinations of means. We determined the mechanism of toxicity via measurements of oxidative stress and metal ions. The toxicity of ZnONPs and TiO2NPs to natural aquatic bacterial assemblages appears to be concentration dependent. Moreover, the cytotoxicity of ZnONPs and TiO2NPs appeared to be affected by HA concentration, the presence of sunlight irradiation, and the dynamic multiple interactions among these factors. With respect to light versus darkness in the control group, the data indicate that bacterial viability was inhibited more in the light exposure than in the darkness exposure. The same was true in the HA treatment groups. With respect to terrestrial versus Suwanee River HA for a given nanoparticle, in light versus darkness, bacterial viability was more inhibited in the light treatment groups containing the terrestrial HA than in those containing Suwanee River HA. Differences in the extent of reactive oxygen species formation, adsorption/binding of ZnONPs/TiO2NPs by HA, and the levels of free metal ions were speculated to account for the observed cytotoxicity. TEM images indicate the attachment and binding of the tested nanoparticles to natural bacterial assemblages. Besides the individual parameter, significant effects on bacterial viability count were also observed in the following combined treatments: HA-ZnONPs, HA-LI, ZnONPs-LI, and HA-ZnONPs-LI. The main effects of all independent variables, plus interaction effects in all cases were significant with TiO2NPs.