Engineered nanomaterials (ENMs) are likely to undergo some degree of modification when released into the environment, which can influence the fate, behavior, and toxicity of nanoparticles (NPs). The environmental factors in natural aquatic ecosystems, such as water chemistry, hydrology, disturbance, and biotic interactions, can transform or “age” toxic chemicals through physical, chemical, and biological processes, including aggregation and disaggregation, adsorption, redox reaction, dissolution, complexation and biotransformation. The extent of aging can vary considerably over time and within a single or a number of water bodies, such as a river that flows into the ocean through an estuary. However, the ecological effects of NPs under realistic environmental exposure scenarios are not yet fully understood. Adding to these challenges are problems arising from traditional ecotoxicological risk assessments, which are inevitably hampered by narrow subsets of relevant species, toxicants, exposure conditions, and levels of impact. The present work examined the toxicity of copper-based nanoparticles (CBNPs), which frequently enter natural aquatic ecosystems due to their increasing application in consumer products, by assessing their impact on marine phytoplankton and estuarine amphipods, organisms that are central to aquatic ecosystems. Standard toxicological methods were used, along with physiological measurements, studies of fate and transport, and mechanistic biological models based on Dynamic Energy Budget (DEB) theory. The aim of the work was to understand 1) the influence of aging processes on CBNPs under environmentally relevant test conditions, 2) the impact of aged CBNPs on a marine phytoplankton population, 3) the potential impact of CBNPs on non-target estuarine organisms, and 4) the potential for detecting and predicting the toxic effects of CBNPs on an individual, to generate model estimates of effects on populations and communities. CBNPs were found to be toxic to benthic estuarine organisms at concentrations of CBNPs already found in the natural environment. However, sublethal toxicity may not be detected by traditional ecotoxicological tests. Additionally, aging was found to influence the fate and transport of CBNPs through oxidation, aggregation, and dissolution processes, increasing Cu toxic ion bioavailability to pelagic organisms over time. While current studies increasingly consider more realistic environmental exposure scenarios, this work, as well as that of other researchers, suggests that CBNPs behave differently under prolonged environmental exposure, and nanoecotoxicological research should focus on sublethal impacts, integrated with mechanistic biological models and based on Dynamic Energy Budget (DEB) theory.