Silver nanoparticles (AgNPs), potent antibiotic materials, have been found to cause cell-membrane damage and produce reactive oxygen species (ROS). The resultant structural change in the cell-membrane could cause an increase in cell permeability of silver ions and AgNPs. To address this issue further, in-vivo and in-vitro cytotoxicity testing of as-made nanomaterials was conducted to quantify and assess their nanotoxicity. Considering the behavior of AgNPs in the environment, toxicity may be reflected by differences in their physicochemical properties (size, agglomeration rate, adsorption properties on humic acid) dependency and toxicity depression. Therefore, we investigated the effect of the cellular uptake of AgNPs with the kinetics of agglomeration and adsorption. The amount of agglomerated and adsorbed AgNPs with sizes of <14 nm was higher than that for AgNPs with sizes of 90 and 140 nm. For 90 and 140 nm sized AgNPs, adsorption was more significant than agglomeration. It is noteworthy that the normal concept that smaller sized AgNPs are taken up more readily may be in error in cases of interactions of abiotic factors.