Lynch served as a temporary New York City magistrate in 1930. He was a delegate to New York's state constitutional convention in 1938.
He was first elected to the 76th United States Congress in a special election to fill the vacancy caused by the death of Edward W. Curley, and was re-elected to the 77th, 78th, 79th, 80th, and 81st U.S. Congresses, in total serving from February 20, 1940, to January 3, 1951.
Lynch was a delegate to the Democratic National Conventions of 1944 and 1948.
Candidate for governor
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In 1950, Lynch was the Democratic nominee for governor of New York, but was defeated in a landslide by incumbent Thomas E. Dewey.
In 1952, Lynch served as chairman of the New York State Democratic Committee. Lynch was elected to the New York Supreme Court in 1954, and served from January 1955 until his death.
Lynch married Claire Rosemary Mitchell (1895–1985) in 1920. They were the parents of sons Walter A. Lynch Jr. (1921–2017) and John Joseph Lynch (1928–1995).