In 2006, Dokken was Associate Director of the Texas A&M University-Corpus Christi Center for Coastal Studies. While working as an adjunct professor at A&M, Dokken was also the Director of the National Oceanic and Atmospheric Administration Gulf of Mexico Regional Marine Research Program. As Executive Director of the Texas State Aquarium in 1985, Dr. Dokken directed the efforts to establish the newly formed nonprofit facility in Corpus Christi, Texas. He is the founder and coordinator of the Flower Garden Ocean Research Program which integrates the efforts of institutional science and the offshore oil and gas industry to expand opportunities for marine research in the most cost-effective manner.