It is widely known that marine habitats are exposed to a wide range of pollutants, and a substantial body of research suggests that these pollutants have a severe impact on the health of associated biota and tertiary consumers as well. Methods, approaches, and technology used to assess pollution levels or impacts are also constantly changing with hundreds of new chemicals originating from commercial, industrial, and urban sources and are introduced into the worldwide market and finding their way into the marine ecosystem as well as impact on coastal biota of benthic ecosystem. This chapter’s also review of the entrance route, the process involved in presence in the benthic food web, and the detrimental effects of heavy metal and microplastics intake on fish highlights the toxic effects on secretion alteration, gene expression (molecular level), cytotoxicity, oxidative damage, inflammatory response, and metabolism (cellular and organ level), as well as individual levels (survival, feeding activity and swimming, energy reserves and respiration, intestinal microorganisms, development and growth, and reproduction). The present review focuses on the marine benthic ecosystem’s Adverse Outcome Pathways (AOPs), which offer insights into the incorporation and transfer of heavy metals and microplastics across several biological organization levels and lastly affect humans as tertiary consumers.