The increasing application of nanomaterials both in commercial and industrial products has led their accumulation in the aquatic ecosystem. The rapid development and large scale production of nanomaterials in the last few decades have stimulated concerns regarding their potential environmental health risks on aquatic biota. Inorganic nanoparticles, due to their unique properties and associated material characteristics resulted in toxicity of these nanomaterials in aquatic organisms. Understanding their novel properties at nanoscale has established to be a significant aspect of their toxicity. Unique properties such as size, surface area, surface coating, surface charge, aggregation of particles and dissolution may affect cellular uptake, molecular response, in vivo reactivity and delivery across tissues of living organism. Already lot of research in the past three or four decades within the nano-ecotoxicology field had been carried out. However, there is not any standard technique yet to assess toxicity of nanoparticles (NPs) on different biological systems such as reproductive, respiratory, nervous, gastrointestinal systems, and development stages of aquatic organisms. Specific toxicological techniques and quantification of nanoparticles are vital to establish regulations to control their impact on the aquatic organism and their release in the aquatic environment. The main aim of this chapter is to critically evaluate the current literature on the toxicity of nanomaterials on aquatic organism.