Many aquatic toxicity experiments are not performed under realistic environmental conditions. We examined several inorganic and organic nanoparticle (NP) formulations (citrate-capped silver NPs, carboxylic acid functionalized single-walled carbon nanotubes, mercaptoundecanoic acid functionalized cadmium selenide NPs, poly(acrylic acid) (PAA)-coated zinc oxide [ZnO] NPs, Nile red-loaded PAA nanocapsules, and uncoated sphere- and leaf-shaped ZnO NPs) to determine whether the presence of humic acid (HA) affects the physicochemical properties (e.g. size, zeta potential, and particle dissolution) of NPs in suspension and ameliorates noted effects on zebrafish (Danio rerio) development. We investigated the toxicological effects of these NPs with and without HA addition during early stages of zebrafish development by measuring survival, hatching success, length, head-tail angle, movement, and protease activity in the chorionic fluid, as well as NP interaction with the chorion. Though NP-induced effects on survival were not mitigated by the presence of HA, hatching inhibition and reduced head-tail angle in developing zebrafish caused by certain NPs were restored to near control values by HA addition. Interestingly, despite the ameliorating effects noted with the addition of HA, combined NP and HA treatments still resulted in reduced enzyme activity and NP interaction with the zebrafish embryo. We suggest that observed effects were NP-specific and not attributed to ionic metal species. In the interest of performing more environmentally representative toxicity studies, HA should be included in standardized laboratory nanotoxicity tests since it alters certain biological effects.