An essential role of the FAMOS international cooperation project is to obtain new marine gravity observations over the Baltic Sea for improving gravimetric geoid modelling. To achieve targeted 5 cm modelling accuracy, it is important to acquire new gravimetric data, as the existing data over some regions are inaccurate and sparse. As the accuracy of contemporary geoid models over marine areas remains unknown, it is important to evaluate geoid modelling outcome by independent data. Thus, this study presents results of a shipborne marine gravity and GNSS campaign for validation of existing geoid models conducted in the eastern section of the Baltic Sea. Challenging aspects for utilizing shipborne GNSS profiles tend to be with quantifying vessel’s attitude, processing of noise in the data and referencing to the required datum. Consequently, the novelty of this study is in the development of methodology that considers the above-mentioned challenges. In addition, tide gauge records in conjunction with an operational hydrodynamic model are used to identify offshore sea level dynamics during the marine measurements. The results show improvements in geoid modelling due to new marine gravimetric data. It is concluded that the marine GNSS profiles can potentially provide complementary constraints in problematic geoid modelling areas.