The squad was taking part in the 2015 World Junior Rowing Championships, held at the weekend on the Rodrigo de Freitas Lagoon in the heart of Rio.
U.S. Rowing said Tuesday it was looking into the cause of the illness and that it was not possible to say what was to blame.
However, incidents in which dead fish have washed up in the lagoon
-- also the venue for Olympic canoeing events -- have previously prompted questions over the safety of the water.
Alarm bells have also sounded over pollution in Guanabara Bay, site of the Olympic sailing events, and Copacabana Beach, where triathletes dived into the surf earlier this month for another pre-Games test event.
Local Olympic officials and Rio's mayor have insisted, however, that the city's waters are safe for competition events and pose no threat to the athletes' health.
'Irresponsible' to blame illness on water
's chief executive Glenn Merry said in a statement that while water in the lagoon may have been the cause of the athletes' sickness, "other sources are also possible."
Athletes have previously fallen ill when traveling to other countries and the cause is sometimes difficult to determine, he said. The squad in Rio had a protocol in place that included washing every piece of equipment after it was used, he added.
"It would be easy but irresponsible for us to immediately assume that the rowing course is the main or sole point of exposure that caused the illnesses. We are not jumping to this immediate conclusion for two reasons," Merry said.
"First, one of our first cases of illness was a coach, who did not row on the lake, and their contact with the course water would have been specific to handling equipment that had been on the water. Assuming sanitation protocol was followed, we would not expect them to become ill.
"Second our female single sculler capsized on the course during her race on Friday. During that immersion event, she consumed some amount of lake water. In speaking with our staff in Rio prior to the team departure Monday night, she had not yet shown any symptoms of illness that our other team members went through."
The World Rowing Federation assured U.S. Rowing that it was testing water in the lagoon every two days in the weeks leading up to the competition and that those tests showed no significant numbers for E. Coli, he added.
Rio mayor: Water quality 'not an issue'
While U.S. Rowing is continuing to review what happened, reports of illness among the team are bound to ring alarm bells in the rowing community.
An investigation commissioned by the Associated Press
, published last month, found Olympic water venues so contaminated with human sewage that it said athletes risked becoming violently ill.
Biologist Mario Moscatelli told CNN last week that his own analysis backed up the findings in the AP report.
Last year, biologists said rivers leading into Guanabara Bay contained a superbacteria that is resistant to antibiotics and can cause urinary, gastrointestinal and pulmonary infections.
"If I fell in this water right now I could contract anything from a conjunctivitis to an intestinal disorder or even hepatitis A," he said.
Only 49% of Rio's homes are connected to sewage lines, and city and state governments have admitted they won't meet cleanup targets ahead of the Games.
But officials say recent water samples show no health risks for athletes.
"It's not an issue for the Games, it's not an issue for the sailors that will come to Rio, that's a lie when people say that. The area where sailing competition is going to be held is a good area, it's a safe area," said Rio de Janeiro Mayor Eduardo Paes.