Nanoparticles (NPs) are the basis of a range of emerging technologies used for a variety of industrial, biomedical, and environmental applications. As manufactured NP production increases, so too does the concern about their release into the environment and potentially harmful effects. Creating nanomaterials that have minimal negative environmental impact will heavily influence the sustainability of nanomaterials as a technology. In order to create such NPs, the mechanisms that govern NP toxicity need to be better elucidated. One aspect of NP structure that may influence toxicity is the identity and charge of ligand molecules used to functionalize the NP surface. These surface chemistries have the potential to increase or decrease negative biological impacts, yet their impacts are poorly understood. In this study, the toxicity of three types of functionalized ~4–5 nm gold NPs (AuNPs), polyallylamine hydrochloride (PAH–AuNPs), citrate (Cit–AuNPs) and mercaptopropionic acid (MPA–AuNPs) as well as cetyltrimethylammonium bromide-functionalized gold nanorods (CTAB–AuNRs) were evaluated in the toxicological model species, Daphnia magna. In order to get the most detailed information on NP toxicity in D. magna, both acute and chronic toxicity assays were performed. Acute exposure toxicity assays show that overall the negatively-charged AuNPs tested are orders of magnitude less toxic than the positively-charged AuNPs. However, chronic exposure assays show that both positively and negatively-charged particles impact reproduction but potentially through different mechanisms and dependent upon functional group. In addition, while select ligands used in NP functionalization (such as CTAB) that are toxic on their own can contribute to observed NP toxicity, our acute toxicity assays indicate that minimally toxic ligands (such as PAH) can also cause significant toxicity when conjugated to NPs. This research demonstrates that surface chemistry plays a pivotal role in NP toxicity and that surface chemistry has the potential to affect the sustainability of these materials. Nano impact Understanding the impacts of engineered NP exposure on aquatic organisms is essential to predict the environmental implications of nanotechnology, however issues with nanomaterial synthesis and characterization often plague these studies. In this study the acute and chronic toxicity of well characterized gold nanoparticles functionalized with ligands of differing charges were investigated in Daphnia magna. We found that AuNP toxicity was highly dependent on both NP charge and ligand identity where positively charged nanomaterials were more toxic and certain ligands were only toxic when associated with the nanomaterial. Select negatively charged nanomaterials also impacted reproduction. This experiment illustrates the need for well-characterized nanomaterials to determine the impacts of nanomaterial properties on toxicity to inform the safe and sustainable development of nanomaterials.