Over a period of just 50 years (from 1960 to 2010) global oceanic oxygen reserves have been reduced by 2% and the anoxic waters have quadrupled, mainly due to anthropogenic global warming and eutrophication. In Danish waters, deoxygenation is an increasing problem with 2023 experiencing the most severe anoxia in 20 years. In the DeoxyMar research cruise, we propose an international collaboration with cooperation partners from Denmark, Germany and Sweden onboard the RV Aurora. Our aim is to provide a mechanistic and quantitative understanding for microbial element cycling interactions under varying levels of deoxygenation. Our cruise plan includes sampling from surface oxic waters to subsurface anoxic sediments at four stations from the seasonally anoxic Mariager Fjord and Aarhus Bay to the Kattegat open water, all in Danish national waters. Furthermore, we will perform incubations during and after the cruise at Aarhus University to target specific microbial groups (e.g. Asgard archaea or cable bacteria) and biogeochemical processes (e.g. sulfur incorporation or methane oxidation). The DeoxyMar research team is made up of PhD students, early career Postdocs, Senior Researchers and Associate Professors who will combine their multidisciplinary expertise in microbiology, geochemistry and oceanography. Overall, we will provide to the international community an ideal model system for investigating how microbes respond to the seasonal development of an oxic-anoxic interface in Denmark, as well as to extrapolate the effects of a global problem such as deoxygenation in Danish national waters to global coastal environments and climate change research.