As part of the NOVANA monitoring project (novana.au.dk), C-POD data loggers (Chelonia Limited) have been deployed in Inner Danish Waters since 2004 to monitor the presence of harbour porpoises (Phocoena phocoena).

Denmark's three most numerous marine mammals are the harbour seal, the grey seal and the harbour porpoise. All three species are protected in Denmark and under the EU Habitats Directive. Harbour porpoises and both seal species are mentioned in the Habitats Directive's annex lists of species in need of protection. Protected areas, so-called habitat areas under Natura 2000, have been designated for all three species. Harbour porpoises must also be protected throughout their entire range, and seal species may require additional management measures if monitoring shows that their range and numbers are declining. In Danish waters, there are also large permanent populations of white-beaked dolphins and minke whales in the Danish part of the northern North Sea and Skagerrak, smaller groups of bottlenose dolphins scattered in Danish waters and individual groups of killer whales, primarily in Skagerrak. All whale species must be protected throughout their entire range.