<p>Shipping operations are essential to global trade and economic growth; however, they pose significant risks to marine ecosystems. The goal of this review was to analyze various categories of shipping operations and their corresponding environmental impacts on marine organisms. The study employs a comprehensive approach that encompasses literature analysis and the synthesis of contemporary scientific findings. This study focused on peer-reviewed articles published from 2000 to 2025 on Web of Science and PubMed. EndNote was used for reference management. The evaluation categorizes shipping operations by ship type and commercial shipping operation type and examines their diverse effects, including chemical and physical pollution. The literature search initially identified 2993 articles. After systematically removing duplicates and evaluating the relevance of each study, the final selection was reduced to 2094 articles. Principal stressors from ship discharges, namely, marine litter, oil spills, ballast water discharge, antifouling paints, sewage, and bilge water, are emphasized for their contributions to habitat degradation, toxicity, and the proliferation of invasive species. VOSviewer software facilitated the creation of visual relatedness maps and timelines for recurring keywords. Physical disruptions from shipbreaking, sinking, underwater acoustics, and artificial lighting further exacerbate the stress on marine animals, influencing their behavior, physiology, and survival. The report assesses the limitations of existing research and regulatory frameworks, highlighting significant knowledge gaps that impede effective mitigation. This review consolidates the knowledge from recent studies and serves as a helpful foundation for marine and environmental scientists and policymakers on shipping operations, biodiversity monitoring, and management techniques for future research.</p>