Nowadays, maritime air pollution is regarded as a severe threat to coastal communities’ health. Therefore, many policies to reduce air pollution have been established worldwide. Moreover, there has been a shift in policy and research attention from greenhouse gases, especially CO2, to other air pollutants. To address the current local environmental challenges, this research analyzes the non-greenhouse gas emissions inventory (CO, NOx, SOx, PM, VOC, and NH3) from ships in the second biggest port in Korea, the Port of Incheon (POI). A bottom-up activity-based methodology with real-time vessel activity data produced by the Vessel Traffic Service (VTS) is applied to obtain reliable estimations. NOx and SOx dominated the amount of emission emitted from ships. Tankers, general cargo ships, cruise ships, and container ships were identified as the highest sources of pollution. Based on the above results, this study discusses the need for long-term policies, such as the designation of a local emission control area (ECA) and the establishment of an emission management platform to reduce ship-source emissions. Furthermore, this study elucidates that significant emissions come from the docking process, ranging from 33.9% to 42.0% depending on the type of pollutant when only the auxiliary engines were being operated. Therefore, short-term solutions like applying exhausted gas cleaning systems, using on-shore power supplies, reducing docking time, or using greener alternative fuels (e.g., liquefied natural gas or biofuels) should be applied and motivated at the POI. These timely results could be useful for air quality management decision-making processes for local port operators and public agencies.