John Watkins did his graduate work in commutative algebra. Soon after joining the department in 1977, he realized the advantages of introducing graph theory to undergraduate study; it is reasonably accessible, and yet there are many unsolved problems. Watkins retrained himself over the next few years in graph theory and pioneered courses in discrete mathematics and graph theory. In 1993, John introduced a course titled Research in Mathematics. He presented the students with problems selected from discrete mathematics and then helped them develop their ideas. The result: several published papers (six as of 1999).

Watkins has continually worked to make mathematical connections with the outside world:

• In 1981, he met Robin Wilson, a graph theorist from the Open University who has visited the college many times over two decades and collaborated with Watkins on a graph theory text (Graphs: An Introductory Approach - 1990).
• In 1985, Watkins became director of the TRIBES program for Native American high school students.
• In 1991, he turned his organizational talents to a summer mathematics and science program he developed for high school students from the San Luis Valley. This program continued each summer through the 1990's.
• In 1992, he was the program organizer for the regional MAA meeting which was held at Colorado College.
• In 1998, he was director of the Associated Colleges of the Midwest Zimbabwe program. Watkins returned to Africa after working there as a Peace Corps volunteer in 1968-1970.

Watkins' organizational skills and appreciation for the arts made him a prime candidate to head the college's summer program; in 1999, he became Dean of the Summer Session. His connection with the mathematics department was by no means severed, but his teaching was reduced to a special course here and there. After three years at the helm of the summer session, he returned to the department in the fall of 2001.