Bowman, who helped record-breaking American Phelps to 18 Olympic gold medals, will work as a consultant to the Turkish programme leading up to the Rio de Janeiro Games in 2016.
"It's exciting for me to take part in this project," Bowman told a news conference on Tuesday at which mobile phone company Turkcell announced an $8 million funding package for improved coaching in swimming and athletics.
"Turkey has a huge potential of swimmers and it's great that the financing from the private sector is used to bring out this potential."
Turkey, a country in which soccer is the dominant sport followed by basketball and volleyball, has never won a swimming medal at the Olympics. High class track and field athletes are also few and far between.
Sports minister Suat Kilic, speaking at the same news conference, said the appointment of Bowman was the start of a recruitment drive aimed at providing Turkey with more Olympic medal prospects at the next two Games.
"Bob Bowman will be a consultant for the Turkish swimming from now on, and will help the sport of swimming in Turkey to improve," he said.
"We will be signing other big names in athletics as well to raise better coaches and athletes."
"We need to select 20,000 elite athletes from 12 million young people in Turkey," Kilic added. "There was something missing in raising our kids to be accomplished swimmers, I think they are all champion candidates.
"Now that the coach of the world's most medal-winning swimmer is the consultant for Turkish swimmers, I think it will be easier to raise the most successful swimmers in the world."
Turkish media earlier reported that Bowman had a 13-article plan to contribute to Turkish swimming, including training camps for swimming coaches in the United States.
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