Mernild's research centers on local, regional, and global modeling using a wide variety of atmospheric and terrestrial models and observations with a specific focus on understanding and simulating climate change interactions related to snow, glacier ice mass-balance (for the Greenland Ice Sheet and mountain glaciers), and freshwater runoff (the water balance components) in Arctic, Antarctic, Patagonia, and the Andes. He has been leading several funded projects and expeditions to these geographical locations.

He has been co-author on different international reports e.g., annual Arctic Card reports from NOAA, and was a contributing author on the latest IPCC report, the AR5 report (Chapter 13). Further, Mernild was co-author on the 'Melting Snow and Ice: A call for action' report. This report was presented by Vice President Al Gore at the UN Climate Change Conference in Copenhagen (COP15).