Gold nanoparticles have been widely used in several areas of human activities, including the biomedical field, due to their small size and unique properties. However, its entrance into the environment may be expected with their increased use. There is thus the need to understand how these nanoparticles used in biomedical applications will affect environmental health, and therefore human health. One of the requirements for using gold nanoparticles is their non-toxic and biocompatible nature to both in vivo and in vitro systems. Some concerns on their possible impact in the environment have been raised with few studies addressing the effects of the particles in marine organisms. This work will present data on the biochemical effects of gold nanoparticles in marine organisms (bivalves and fish), alone and combined with other environmental contaminants. Overall, data show that the particle stability in high ionic strength media and the observed effects are highly dependent on the surface coating. Nonetheless, the studied nanoparticles proved able to induce peroxidative damage both in bivalves and fish, and to promote alterations in neurotransmission. Although the benefits of these nanomaterials are extensively shown, their unintentional release or disposal deserve more care and precaution.