The marine environment faces a pressure from the increasing shipping intensity in the form of rising levels of continuous anthropogenic underwater noise. Current underwater noise monitoring guidelines advise to measure the long-term trends in the overall noise levels in the frequency bands where ship noise is most prevalent. However, the natural noise is omnipresent and prolongs the time period required for the detection of statistically significant trends in the overall noise. The monitoring efficiency can be improved by finding the proportions of the anthropogenic and the natural noise levels and by measuring the changes in the proportions over time. These proportions can be found by differentiating between the two types of ambient noise in the recordings according to both proximity of the ships and the variability of the environmental conditions. This is achieved by using the AIS ship traffic data along with the ship noise detection algorithms. The AIS data enable to determine the position of ships around a noise monitoring location and calibrate the ship noise detection algorithms. The results and the methods are presented for the passive acoustic monitoring in the Baltic Sea and applicability of the described methods are discussed.