In 1937 he was invited by rheumatologist Walter Bauer to work at Massachusetts General Hospital and perform research on lupus erythematosus. When war broke out in 1939, Bywaters returned to Britain, but was not taken into the army because of kidney problems and instead took over Rheumatology at the British Postgraduate Medical School at Hammersmith Hospital. During the bombing of London, he clarified that so-called crush syndrome was renal failure in wounded bomb victims who had been freed from crushing injuries. Bywater traced the condition to the release of myoglobin from injured muscle tissue entering the bloodstream. He found a method of treatment in the form of intravenous or oral administration of alkaline fluids.
After the war, he built up rheumatology as an independent medical discipline. In 1947, he became director of a small hospital department for rheumatism sufferers at the Canadian Red Cross Memorial Hospital in the village of Taplow, near Maidenhead in Berkshire. Immediately after the discovery of the therapeutic effect of cortisone against rheumatic fever by Philip Showalter Hench and Edward Calvin Kendall he undertook clinical tests that confirmed this (participation in 1948). The approach of treating rheumatic heart disease using cortisone, was eventually made irrelevant by the availability of antibiotic treatment, which nearly eliminated the disease in the UK and other developed countries. Bywaters used his expertise as a pathologist for accurate characterization of rheumatic diseases and to develop new methods of treatment of chronic arthritis in children and adolescents.
His hobbies were gardening and painting.