The harbor construction projects can lead to various marine environmental problems including habitat degradation and loss, marine water pollution, change of flow patterns, erosion, scour, sedimentation, and so on. The EIA is a measure to prevent various environmental problems in advance from examining and minimizing the environmental impacts before the proposed developments are implemented. In addition, institutions reviewing EIA reports have made efforts to conduct scientific and standardized EIA by applying EIA guidelines for each project. This study aims to create a EIA guideline focusing on the harbor construction projects. Based on the review comments of the harbor construction EIA reports for the past 13 years (2009-2021) and the EIA guidelines of different types of projects, we identified the marine environmental problems and provided the appropriate guideline. This guideline summarizes and presents the contents which must be reviewed in the baseline condition survey, impact assessment, mitigation, and postenvironmental impact investigation in the fields of marine fauna and flora, marine physics, and marine water and sediment quality. In the case of a baseline condition survey of marine fauna and flora, a method for selecting survey points considering the characteristics of sea area and project was presented. When estimating the impact of marine fauna and flora, we presented methods for predicting the impact on them due to the spread of suspended sediments and the damage to benthic habitats due to dredging and reclamation. In consideration of the characteristics of the sea area, we divided the survey items of the marine physics into essential items and supplementary items. In predicting the impact of marine physics, various methods for major issues such as seawater circulation, suspended sediment and bottom sediment transport, water temperature and salinity diffusion, seawater exchange, wave transformation, harbor tranquility, and shoreline change were presented. The research results will contribute to protect the marine environment by inducing more systematic and scientific surveys, impact assessments, and mitigation in the EIA process.