Shipborne gravimetry is an essential method to measure the Earth’s gravity field in the coastal and offshore areas. It has the special advantages of high-accuracy and high-resolution measurements in coastal areas compared to other techniques (e.g., satellite gravimetry, airborne gravimetry, and altimetry) used to obtain information about the gravity field. In this paper, we present the data processing strategies of shipborne gravimetry in GFZ. One key point is that the most suitable filter parameters to eliminate disturbing accelerations are determined by studying the GNSS-derived kinematic vertical accelerations and the measurement differences at crossover points. Apart from that, two crucial issues impacting on shipborne gravimetry are the seiches in some harbors and the squat effect in the shallow water. We identified that inclusion of GNSS-derived kinematic vertical accelerations can help to improve the shipborne gravimetry results at these special cases in the Baltic Sea. In the absence of the GNSS-derived vertical accelerations, the cutoff wavelength of the low-pass filter should be large enough to filter out these disturbing acceleration signals which causes a coarser spatial resolution of the gravity measurements. Therefore, the GNSS-derived kinematic vertical accelerations are very useful for optimum shipborne gravimetry. Finally, our shipborne gravimetry measurements are successfully used to verify the previous gravimetry data and improve the current geoid models in the Baltic Sea.