Seabed surveying is the basis of engineering development in shallow waters. At present, geophysical survey methods mainly utilize sonars for qualitative surveying, which requires the calibration of the results found through in situ drilling and sampling. Among them, the parameters required for engineering designs are obtained from either in situ tests or laboratory experiments of soil samples retrieved from drilling. However, the experience from onshore applications shows that the physical quantities obtained through quantitative geophysical survey methods for shallow waters can be indirectly used to estimate engineering parameters or directly as parameters for engineering evaluation, which has high application potential. This review analyzes various geophysical survey methods for nearshore site characterization (i.e., side-scan sonar, single/multi- beam sonar, sub-bottom profiler, seismic reflection method, and underwater magnetometer) and challenges in their application, and introduces quantitative geophysical survey methods (including the underwater seismic refraction method, seismic surface wave method and underwater electrical resistivity tomography) that are worth focusing on for future development. Three application difficulties have been identified, namely, the lack of operational efficiency, appropriate operational equipment and systems, and sufficient guidance for experimental shallow sea applications. It is hoped that comprehensive discussion of these challenges will increase awareness leading to engineering improvements in the surveying and measuring capabilities in shallow waters, further reducing the risk of geotechnical hazards.