Nanoparticle (NP) physiochemical properties have been shown to be important determinants of NP interactions with biological systems. Due to both nanomaterial diversity and environmental complexity, a mechanistic understanding of how physiochemical properties affect NP/organism interactions will greatly aid in the accurate assessment and prediction of current and emerging NP-induced environmental impacts. Herein, we investigated key biological apical endpoints, such as viability, growth, and reproduction and the expression of genes associated with related molecular pathways in response to exposure to gold nanoparticles (AuNPs) functionalized with either positively charged ligands, polyallyamine hydrochloride, or negatively charged ligands, mercaptopropionic acid, in two model organisms, the bacterium Shewanella oneidensis MR-1 and the water flea Daphnia magna. By linking changes in molecular pathways to apical endpoints, potential biomarkers for functionalized AuNP impacts were identified in both organisms. Specifically, act was identified as a potential biomarker in D. magna and 16S as a potential biomarker in S. oneidensis. We also revealed that changes in molecular pathways induced by ligand-NP combination were strongly dependent upon the type of ligand on the NP surface, and the effects from their respective ligands alone might predict these effects for the ligand-NP combination, but only in some cases. Lastly, we revealed that it is possible to identify similar pathways provoked upon NP exposure across organisms. This study shows that molecular pathways will help elucidate mechanisms for NP toxicity that are predictive of adverse environmental outcomes.