Increasing levels of priority pollutants such as polycyclic aromatic hydrocarbons (PAHs), pesticides and emerging pollutants like pharmaceuticals and personal care products, plastics, polychlorobiphenyls, among others, have been observed in the Lagos lagoon, Nigeria. This is a cause for concern due to the cumulative and long-term adverse impacts on fisheries, other aquatic life and human beings whose livelihoods depend on these resources and who consume the fisheries. Therefore, there is an urgent need for contextual standards and frameworks for the management of this highly important aquatic ecosystem in Nigeria.