The escalating global contamination of aquatic ecosystems by pharmaceuticals and endocrine-disrupting chemicals (EDCs) stemming from diverse anthropogenic sources represents a critical and pervasive threat to planetary Earth. These contaminants exhibit bioaccumulative properties in long-lived organisms and undergo trophic biomagnification, leading to elevated concentrations in apex predators. This review synthesizes current knowledge regarding the far-reaching impacts of pharmaceutical and EDC pollution on the reproductive biology of aquatic fauna, focusing on the heightened vulnerability of the endangered African penguin. A rigorous literature review across key scientific databases—PubMed, Scopus, Web of Science, and Google Scholar—using targeted search terms (e.g., penguins, contaminants of emerging concern, penguin species, seabird species, Antarctica, pharmaceuticals, personal care products, EDCs) underpins this analysis. This review explores the anthropogenic sources of pharmaceuticals and EDCs in aquatic ecosystems. It discusses the mechanisms by which these chemicals disrupt the reproductive physiology of aquatic fauna. Recent studies on the ecological and population-level consequences of these contaminants are also reviewed. Furthermore, the review elaborates on the urgent need for comprehensive mitigating strategies to address their effects on vulnerable penguin populations. These approaches hold the potential to unlock innovative pathways for conservation initiatives and the formulation of robust environmental management policies aimed at safeguarding aquatic ecosystems and the diverse life they support.