The Little Britain comic suffered severe vomiting and diarrhoea after swallowing some of the river's water, which contains bacteria such as E.coli and salmonella.
Walliams, who received medical attention throughout the day on Wednesday, has now fallen behind schedule in the eight-day, 140-mile swim.
"I always knew there was a risk that taking in the water could cause problems, but now it's happened it has hit me really hard," he admitted. "I was sweating in the night and have been to the toilet a lot this morning."
Walliams, who swam the English Channel in 2006 for the same charity, added: "This is already much harder than I thought it would be. This Thames tummy I've got is making the task seem incredibly difficult. London seems a long way away."
However, the Come Fly with Me star revealed that the support of the public has helped overcome the setback.
"When I heard the total raised had jumped to more than £200,000 it gave me a real boost, as do the thousands of people who have been turning out and cheering," he added. "There were so many last night I thought Take That were in a boat behind me."
The BT Sport Relief Challenge: Walliams vs The Thames will be broadcast in the run-up to Sport Relief in March 2012.
To sponsor Walliams's swim, visit the Sport Relief website.
> David Walliams: 'Swimming stops me partying'
Watch David Walliams attempt to overcome his stomach bug on the third day of his Thames swim for Sport Relief below: