Since returning to New Zealand, McDowell has had a prominent role in the field of land and water resources, becoming a principal scientist at AgResearch. In 2010 he was appointed an adjunct professor and in 2014 he was made a full professor in the Department of Soil and Physical Sciences at Lincoln University.[6][7] In 2014, he was appointed chief scientist of the National Science Challenge: Our Land and Water.[2] In June 2021, McDowell was appointed editor-in-chief of the Journal of the Royal Society of New Zealand.[8]