Recently collected data have shown that natural organic matter (NOM) source is an important parameter influencing the toxicity of silver to the freshwater crustacean Daphnia magna. The present study attempted to correlate the physicochemical properties of 11 naturally isolated and commercially available NOM sources with their ameliorative effects. The protection offered by these samples was standardized to the protective effect of Aldrich humic acid using geochemical modeling approaches that accounted for associated changes in water chemistry and, consequently, silver speciation. The protective ability of NOM was not correlated with reactive sulfide or nitrogen content, which are considered to be strong silver-binding ligands. Color (specific absorbance coefficient) was positively correlated with protection but narrowly eluded statistical significance. The peak wavelength of emission fluorescence following excitation at 370 nm and the fluorescence index values of NOM samples were significantly correlated with protective effects, suggesting that aromatic carbon content may govern the ameliorative actions of NOM. Simple optical properties may therefore act as a suitable indicator for the ability of a given NOM to protect against waterborne silver toxicity to D. magna as long as changes in water chemistry and, thus, silver speciation, are considered.