In 1916 Watson-Watt wanted a job with the War Office, but nothing obvious was available in communications. Instead he joined the Meteorological Office, who were interested in his ideas on the use of radio for the detection of thunderstorms. Lightning gives off a radio signal as it ionizes the air, and he planned on detecting this signal in order to warn pilots of approaching thunderstorms. His early experiments were successful in detecting the signal, and he quickly proved to be able to do so at long ranges. Two problems remained however. The first was locating the signal, and thus the direction to the storm. This was solved with the use of a directional antenna, which could be manually turned to maximize (or minimize) the signal, thus "pointing" to the storm. Once this was solved the equally difficult problem of actually seeing the fleeting signal became obvious, which he solved with the use of a cathode-ray oscilloscope with a long-lasting phosphor. Such a system represented a significant part of a complete radar system, and was in use as early as 1923. It would, however, need the addition of a pulsed transmitter and a method of measuring the time delay of the received radio echos, and that would in time come from work on ionosondes.

At first he worked at the Wireless Station of Air Ministry Meteorological Office in Aldershot, England. In 1924 when the War Department gave notice that they wished to re-occupy their Aldershot site, he moved to Ditton Park near Slough in Berkshire. The National Physical Laboratory (NPL) already had a research station there. In 1927 they were amalgamated as the Radio Research Station, with Watson-Watt in charge. After a further re-organisation in 1933, Watson-Watt became Superintendent of the Radio Department of NPL in Teddington.

In 1934, the Air Ministry set up a committee chaired by Sir Henry Tizard to advance the state of the art of air defence in the UK. During World War I, the Germans had used Zeppelins as long-range bombers over London and other cities and defences had struggled to counter the threat. Since that time aircraft capabilities had improved considerably, and existing weapons were unlikely to have any effect on a raid. The prospect of aerial bombardment of civilian areas was causing the government anxiety with heavy bombers able to approach from altitudes that anti-aircraft guns of the day were unable to reach. With the enemy airfields only 20 minutes away, the bombers would have dropped their bombs and be returning to base before the intercepting fighters could get to altitude. The only solution would be to have standing patrols of fighters in the air at all times, but with the limited cruising time of a fighter this would require a gigantic standing force. A plausible solution was urgently needed.

Nazi Germany was rumored to have a "death-ray" using radio waves that was capable of destroying towns, cities and people. In January 1935, H.E. Wimperis, Director of Scientific Research at the Air Ministry, asked Watson-Watt about the possibility of building their version of a death-ray, specifically to be used against aircraft. Watson-Watt quickly returned a calculation carried out by his assistant, Arnold Wilkins, showing that the device was impossible to construct, and fears of a Nazi version soon vanished. However he also mentioned in the same report: "Meanwhile attention is being turned to the still difficult, but less unpromising, problem of radio detection and numerical considerations on the method of detection by reflected radio waves will be submitted when required."

On 12 February 1935, Watson-Watt sent a secret memo of the proposed system to the Air Ministry, entitled Detection and location of aircraft by radio methods. Although not as exciting as a death-ray, the concept clearly had potential but the Air Ministry, before giving funding, asked for a demonstration proving that radio waves could be reflected by an aircraft. This was ready by 26 February and consisted of two receiving antennas located about ten km away from one of the BBC's shortwave broadcast stations at Daventry. The two antennas were phased such that signals travelling directly from the station cancelled themselves out, but signals arriving from other angles were admitted, thereby deflecting the trace on a CRT indicator (passive radar). Such was the secrecy of this test that only three people witnessed it: Watson-Watt, his assistant Arnold Wilkins, and a single member of the committee, A.P. Rowe. The demonstration was a success; on several occasions a clear signal was seen from a Handley Page Heyford bomber being flown around the site. Most importantly, the prime minister, Stanley Baldwin, was kept quietly informed of radar's progress. On 2 April 1935, Watson-Watt received a patent on a radio device for detecting and locating an aircraft.

In mid-May 1935, Wilkins left the Radio Research Station with a small party, including Edward George Bowen, to start further research at Orford Ness, an isolated peninsula on the coast of the North Sea. By June they were detecting aircraft at 27 km, which was enough for scientists and engineers to stop all work on competing sound-based detection systems. By the end of the year the range was up to 100 km, at which point plans were made in December to set up five stations covering the approaches to London.

One of these stations was to be located on the coast near Orford Ness, and Bawdsey Manor was selected to become the main centre for all radar research. In an effort to put a radar defense in place as quickly as possible, Watson-Watt and his team created devices using existing available components, rather than creating new components for the project, and the team did not take additional time to refine and improve the devices. So long as the prototype radars were in workable condition they were put into production. They soon conducted "full scale" tests of a fixed radar radio tower system that would soon be known as Chain Home, an early detection system that attempted to detect an incoming bomber by radio signals. The tests were a complete failure, with the fighter only seeing the bomber after it had passed its target. The problem was not the radar, but the flow of information from trackers from the Observer Corps to the fighters, which took many steps and was very slow. Henry Tizard with Patrick Blackett and Hugh Dowding immediately set to work on this problem, designing a 'command and control air defence reporting system' with several layers of reporting that were eventually sent to a single large room for mapping. Observers watching the maps would then tell the fighter groups what to do via direct communications.

By 1937 the first three stations were ready and the associated system was put to the test. The results were encouraging and an immediate order by the government to commission an additional 17 stations was given, resulting in a chain of fixed radar towers along the east and south coast of England. By the start of World War II, 19 were ready to play a key part in the Battle of Britain, and by the end of the war over 50 had been built. The Germans were aware of the construction of Chain Home but were not sure of its purpose. They tested their theories with a flight of the Zeppelin LZ 130, but concluded the stations were a new long-range naval communications system.

As early as 1936, it was realized that the Luftwaffe would turn to night bombing if the day campaign did not go well, and Watson-Watt had put another of the staff from the Radio Research Station, Edward Bowen, in charge of developing a radar that could be carried by a fighter. Night time visual detection of a bomber was good to about 300 m, and the existing Chain Home systems simply didn't have the accuracy needed to get the fighters that close. Bowen decided that an airborne radar should not exceed 90 kg (200 lb in weight, 8 ft³ (230 L) in volume, and require no more than 500 watts of power. To reduce the drag of the antennas the operating wavelength could not be much greater than one m, difficult for the day's electronics. "AI" - Airborne Interception, was perfected by 1940, and was instrumental in eventually ending the Blitz of 1941. Bowen also fitted airborne radar to maritime patrol aircraft (known in this application as "ASV" - Air to Surface Vessel) and this eventually reduced the threat from submarines.

In his English History 1914 - 1945, historian A.J.P. Taylor paid the highest of praise to Watson-Watt, Sir Henry Tizard and their associates who developed and put in place radar, crediting them with being fundamental to victory in World war II.

In July 1938 Watson-Watt left Bawdsey Manor and took up the post of Director of Communications Development (DCD-RAE). In 1939 Sir George Lee took over the job of DCD, and Watson-Watt became Scientific Advisor on Telecommunications (SAT) to the Air Ministry, travelling to the USA in 1941 in order to advise them on the severe inadequacies of their air defense efforts illustrated by the Pearl Harbor attack. His contributions to the war effort were so significant that he was knighted in 1942.

Ten years after his knighthood, Watson-Watt was awarded £50,000 by the British government for his contributions in the development of radar. He established a practice as a consulting engineer. In the 1950s moved to Canada. Later he lived in the USA, where he published Three Steps to Victory in 1958. Around 1958 he appeared as a mystery challenger on the American television program To Tell The Truth.

On one occasion, late in life, Watson-Watt reportedly was pulled over in Canada for speeding by a radar-gun toting policeman. His remark was, "Had I known what you were going to do with it I would never have invented it!" He wrote an ironic poem ("Rough Justice") afterwards:

Pity Sir Robert Watson-Watt,

strange target of this radar plot

And thus, with others I can mention,

the victim of his own invention.

His magical all-seeing eye

enabled cloud-bound planes to fly

but now by some ironic twist

it spots the speeding motorist

and bites, no doubt with legal wit,

the hand that once created it.