He was elected to the New Jersey General Assembly from the district encompassing Salem County in 1953. He defeated Republican Peter B. Hoff, who had served as an Assemblyman since 1944.
Waddington was elected to the New Jersey State Senate in 1955, representing Salem County. He defeated incumbent Republican Senator John M. Summerill by 1,138 votes, 9,836 to 8,698. He was re-elected in 1959, defeating former Assemblyman Hoff by 4,043 votes, 12,215 to 8,172. He won a third term in 1963, defeating Republican Joseph Narrow by 5,253 votes, 13,665 to 8,412. He had to run again in 1965 after the U.S. Supreme Court, in Reynolds v. Sims, required redistricting by state legislatures for congressional districts to keep represented populations equal, as well as requiring both houses of state legislatures to have districts drawn that contained roughly equal populations, and to perform redistricting when needed. Because of its population, Salem and Cumberland counties were merged into one district with one Senator. Cumberland County was represented by Senator Robert H. Weber, a Democrat from Greenwich Township. Since both Salem and Cumberland Counties were being merged, only one Democratic Senator could represent the party. In order to avoid a primary election fight between Waddington and Weber, the Democratic party bosses got together in a meeting and decided that Waddington would be the candidate. Weber was made Waddington's campaign manager. The Democrats, thinking that they had avoided a primary fight, were met with yet another surprise. Another Quaker who attended the Salem Friends Meeting with John Waddington, threw his hat in the ring in the Democratic Primary. He was Kenneth R. Jones of Greenwich. He was a school teacher from Bridgeton and had previously taught in Salem. He declared himself as an "Independent Democrat." Mr. Jones carried a lot of support amongst the school teachers in both counties. However, Waddington beat Jones soundly in the June primary with Jones getting just under 1000 votes as compared to Waddington getting over 3000 votes. In the general election, John A. Waddington defeated Cumberland County Republican Chairman John J. Spoltore, a former Mayor of Bridgeton, by 7,902 votes, 32,292 to 24,390. He won Salem County by a 2-1 margin, and carried Cumberland by a narrow 577 vote margin. Waddington served as Senate Minority Leader in 1958 and 1966, and as the Senate Majority Leader in 1967. New rounds of court battles and redistricting forced Waddington to run again in 1967, in an election cycle that was less favorable toward Democrats. This time Waddington ran in the 3rd district, specifically Assembly district 3A, which included all of Salem County and part of Gloucester County. He was defeated by two-term Republican Assemblyman John L. White by 4,830 votes, 28,456 to 23,635. Waddington won Salem County by 3,328 votes, but White's margin in the Gloucester County part of the district was 8,149.
Salem County Freeholder
After losing his Senate seat, Waddington was elected to the Salem County Board of Freeholders and served as Freeholder Director.
In 1973, Waddington explored a bid for the Democratic nomination for Governor of New Jersey. He was one of five candidates to be interviewed by a special committee of ten Democratic County Chairmen formed by Democratic State Chairman Salvatore Bontempo in an effort to unite the party establishment behind a single challenger to Republican Governor William T. Cahill. Waddington decided against entering the race, which was ultimately won by Brendan Byrne.
Governor Byrne appointed him to serve as the Director of the New Jersey Division of Motor Vehicles in 1974. His nomination was confirmed by the State Senate 39-0.
