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The implementation of nautical bottom in port areas characterised by muddy seabed has been discussed within the past tens of years. The nautical bottom is defined as a critical depth limit beyond which contact with a ship's keel causes either damage or unacceptable effects on controllability and manoeuvrability. In many cases, it is described in terms of sediment density criteria representing a specific area, obtained from either on-site physical measurement using mechanical instruments or laboratory tests of sampled sediments. However, the definition of nautical bottom still lacks comparison with the widely used acoustic measurement through echo-sounding. In this paper, we discuss results from geotechnical drilling and free-fall cone penetrometer probing to estimate the nautical bottom and its density criteria, as well as a hydrographic survey by means of echo-sounding. The study area is a low gradient, shallow, and mud-dominated seabed in the Patimban port development area, north of West Java, Indonesia. Samples of seabed from geotechnical drilling facilitate the development of a calibration curve to empirically relate the sampled sediments' undrained shear strength and density obtained from laboratory tests. The calibration curve is used to estimate density profiles from undrained shear strength profiles obtained from the free-fall cone penetrometer. Undrained shear strength profiles from 46 stations are converted into density profiles and their vertical gradient to detect the boundary between the water and the top-most seabed layer, i.e., the nautical bottom. Along with the deployment of the free-fall cone penetrometer, a dual-frequency echosounder survey is launched. The detected nautical bottom in each station is compared to the depths obtained from the dual-frequency echo-sounding. It is advised that the nautical bottom in our study area shall be associated with sediment density criteria of 1.29–1.33 t/m3. The nautical bottom typically lies at about the upper one-fourth of the approximately 0.4 m separation of acoustic depths observed from the high- and low-frequency returns from the dual-frequency echosounder. This finding confirms that high-frequency echo-sounding tend to underestimate the nautical bottom in muddy areas, while the low-frequency tend to overestimate it. The agreement between acoustic and nautical depth seems to be influenced by seabed sediment density. In an area with higher sediment density (1.31–1.33 t/m3), the coefficients of determination, r 2, between nautical and acoustic depths are 0.94 and 0.87 for the high- and low-frequency returns, respectively. On the other hand, in an area with lower sediment density (1.29–1.31 t/m3), the coefficients are reduced to 0.15 and 0.12 for the high- and low-frequency returns, respectively. The work presented in this paper offers a supporting procedure to cope with the uncertainty of seabed detection performed by hydrographic surveys across a muddy and shallow coastal environment. Seabed surveys through echo-sounding in areas equivalent to where this study is carried out should be accompanied by physical seabed probing to assure the accuracy of bottom detection. [ABSTRACT FROM AUTHOR]