Globally nanotechnology has transformed many sectors of human endeavour due to the innovative introduction of different unique materials and products in various areas. Presently large quantities of nanomaterials are synthesized and are essential for several industrial applications. This facilitates and enhances research in biophysics, biochemistry, wastewater treatment, etc. Nanotechnology and other science-related discipline have been combined to synthesize novel nanomaterials through modification of their shapes, composition, and dimension which can be used for various applications in medicines, agriculture, environmental remediation, etc. Despite their peculiar advantages and wide application in several industrials and domestic sectors, fabricated materials of nano-size scale have been raising concerns of unsafety for both human and aquatic biota, due to their incessant release into the aquatic ecosystem. These nanomaterials are ingested by the aquatic biota, from which they bioaccumulate in the organism’s body and hence pass to humans via the food chain. Within the organism’s body, nanomaterials serve as foreign material with different physicochemical characteristics because of their peculiar small sizes. Thus, the harmful effect of nanomaterials on aquatic biota has been generating great concern among the scientific communities. Thus, they can interfere with the normal mechanisms of physiological activities. The present chapter focuses on the sources of the nanomaterials in the aquatic ecosystem, the route of exposure, their process of transformation and interactions, their possible toxicity to the aquatic biota, challenges posed by the nanomaterials, and prospects.