He took up coaching during his time with the Albany Capitals and focused on it fully when he retired from playing. After spending time working in Japan, he returned to America to coach, firstly in Arizona and then at Harvard University. He joined Major League Soccer club New England Revolution in 2004 as a member of Steve Nicol's coaching staff. After five years in Massachusetts, Mariner returned to Plymouth Argyle in 2009 as their head coach. He succeeded Paul Sturrock as the club's manager two months later before returning to his role as head coach upon the arrival of Peter Reid. In January 2011, he returned to Major League Soccer as director of player development at Toronto FC.