The course was designed by golf architect Joe Lee, noted for his work on the NCR Golf course in Dayton, Ohio, home of the 1969 PGA Championship. After seeing Banyan for the first time, Lee was quoted as saying "This place is majestic! All you have to do is listen and the land will tell you what to do". Lee thought the shell pits presented opportunity to allow for rare elevation. The 13th tee, with its 36 foot elevation was at one time the highest elevation in South Florida.
Lee laid out the course like a "string of pearls" - with very few holes designed to be parallel or even close to each other. Many native tropical foliage plants and beautiful cypress trees were salvaged to create a wonderful course. Over 1,000 trees were transplanted at Banyan during the construction of I-95, saved from the advancing backhoes.