An electronic navigational chart is a major source of information for the navigator. The component that contributes most significantly to the safety of navigation on water is the information on the depth of an area. For the purposes of this article, the authors use data obtained by the interferometric sonar GeoSwath Plus. The data were collected in the area of the Port of Szczecin. The samples constitute large sets of data. Data reduction is a procedure to reduce the size of a data set to make it easier and more effective to analyse. The main objective of the authors is the compilation of a new reduction algorithm for bathymetric data. The clustering of data is the first part of the search algorithm. The next step consists of generalisation of bathymetric data. This article presents a comparison and analysis of results of clustering bathymetric data using the following selected methods: K-means clustering algorithm, traditional hierarchical clustering algorithms and self-organising map (using artificial neural networks).