The increased use of Engineered Nanomaterials (ENMs) and their availability in a large number of consumer-based products raises a major alarm for humans and especially for aquatic environments as the potential effects of these ENMs have been poorly characterized. Currently, the limitation of the published data or conflicting published data on the adverse effects of ENMs make it complicated to understand or generalize the risk auxiliary with ENMs to humans and aquatic environment. Due to the large number of ENMs and other chemical products currently in use, high throughput screening (HTS) techniques are clearly needed as the traditional in vivo set up is laborious and time consuming. HTS is an emerging tool to assess biochemical screening that can analyse cellular and biochemical responses in a timely, cost-effective and less laborious manner through digital mechanisms and miniaturization. HTS assays are very helpful to develop chemical libraries that give detailed information on potentially toxic compounds and their dose-dependant profiles and to establish hazardous ranking of NMs through generation of a biological and environmental database. In this respect, the advantages and challenges of HTS, the role of HTS role, and different techniques in addressing emergent contaminations such as ENMs for ecotoxicity are discussed in detail in this chapter.