Generating appropriate ecological risk assessments to support the rapid growth of nanotechnology requires a comprehensive understanding of the potential effects of engineered nanomaterials (ENMs), both toxic and beneficial, and accurate predictions of their environmental concentrations. While significant data exists for widely used nanomaterials, there remains a critical knowledge gap regarding the environmental and biological impacts of emerging ENMs, including graphene oxide, nanodiamonds, carbon nanotubes, and less common metal and metal oxides. This review aims to synthesize current knowledge on the ecological risks of emerging ENMs in aquatic environments. The concentrations are likely to be below common toxicological endpoints. In addition, for some of them there is the potential for hormesis: a beneficial dose that promotes growth of the organisms. Novel approaches, such as the “omics,” can elucidate these effects. The review identifies key knowledge gaps, such as the necessity for better information on the effects of nanomaterial mixtures and the potential effects of organisms on the fate of ENMs, as well as for better models for estimating biomagnification. While the integration of artificial intelligence will serve to close these knowledge gaps, more standardized toxicity testing protocols are required to expand the number of studies that can be used to train machine learning models