The sediment pollution of the aquatic environment by waste due to anthropogenic activity is of an increasing concern. The contaminants coming from the aquatic environment can enter the aquatic food chain and accumulate in the tissues of fish and shellfish used for human consumption. The aim of this study was to sum up the current level of knowledge concerning the pollution of aquatic sediments and its transfer to aquatic foods as well as to indicate whether such contamination has the potential to affect the health and welfare of aquatic organisms as well as the quality and safety of the species intended for human consumption. Based on the results of scientific studies, the European Food Safety Authority, and the Rapid Alert System for Food and Feed, contamination of fish and seafood occurs predominantly through their diet and the levels of bioaccumulative contaminants are higher in fish which rank higher in the food chain. Contamination of aquatic habitats can not only significantly affect behavior, development, and welfare of aquatic organisms, but it can also affect the safety of fish and seafood for human consumption.