The firm of Toomey & Flynn produced many notable golf courses in the Philadelphia area and beyond. William S. Flynn took the lead on course design, while Howard Toomey's responsibilities mainly involved course construction. Flynn's best known designs include, but are not limited to:

UNITED STATES: Atlantic City CC, NJ (1925, modifications) / Boca Raton Resort, FL (1926, Resort course) / Cherry Hills, CO (1922) / Columbia, MD (1935, modifications) / The Country Club-Brookline, MA (1927, Primrose-nine) / The Country Club-Pepper Pike, OH (1930) / Homestead, VA (1923, Cascades course) / Huntingdon Valley, PA (1927) / Indian Creek, FL (1928) / Kittansett, MA (1922, with Fred Hood) / Lancaster, PA (1919) / Normandy Shores, FL (1941) / Pine Meadow, IL (1929, redesign) / Rolling Green, PA (1925) / Seaview, NJ (1927, Pines course, first nine holes) / Shinnecock Hills, NY (1931).

Flynn was one of the most respected and influential of the "Philadelphia School" of golf course design. As a prominent architect in the Philadelphia area he designed nearly 60 courses, although his most renowned work is found outside the area, in layouts such as Cherry Hills (Denver), The Cascades (Virginia), The Country Club (Brookline, near Boston) and Shinnecock Hills (Long Island).

Flynn graduated from Milton High School, where he had played competed against his friend Francis Ouimet. Flynn laid out his first course at Hartwellville, Vermont, in 1909. He then assisted Hugh Wilson on the completion of Merion GC's East course. As a result of his work at Merion, Flynn found his services as a course architect much in demand. He and Wilson had hoped to form a design partnership, but this was prevented by Wilson's failing health. Following World War I, Flynn joined forces with Wilson's friend Howard Toomey, a prominent civil engineer. Flynn was very much responsible for the course architecture, while the implementation and building of his designs was handled by the firm of Toomey & Flynn, in which Howard Toomey led the course construction work. The firm engaged a number of assistants, some of whom, like William Gordon, Robert (Red) Lawrence and Dick Wilson later became prominent designers in their own right.

After course design, Flynn's second love was the art of greenkeeping. He lectured on the subject and wrote many articles and pamphlets describing greenkeeping techniques.