Nilsen's work is focussed on two main subjects, thermohaline circulation in the Nordic Seas and regional sea level change.

About 2/3 of the Atlantic Water entering the Arctic Mediterranean is transformed and return as Overflow Water feeding the deep branch of the AMOC. Nilsen and co-authors address the transformation by reviewing and quantifying from observations and ocean models the relative contributions from the different processes that modify water masses, densify surface waters, and contribute to the ventilation of the Arctic Mediterranean. Assessing the relative contributions from these processes is of key importance for understanding the northernmost limb of the AMOC.

The sea level is rising due to increasing ocean temperatures and melting of land based ice. At the same time different land areas are still rising after the retreat of the last glacial ice sheets. Among other factors affecting sea level rise regionally are ocean temperature distribution by ocean currents and changing heating patterns, freshwater discharges (floods and coastal current), as well as possible changes in storm surges. In the project Sea Level Rise (Endringer i fortidens, dagens og framtidig havnivå med spesielt fokus på vestlandskysten) funded by Bergen municipality, researchers from the Bjerknes and Nansen centers aim to improve the future predictions of sea level rise for the coast of western Norway and neighbouring regions. Using all available data for the different factors behind sea level rise, the project will assess its development over the last 50 years, establish the status of today, and make projections for the 21st and 22nd century.