He met firefighters, police officers and soldiers on the outskirts of the village near Doncaster, then headed to the worst-affected areas.
Clarence House confirmed that Charles had made donations to flood relief funds in South Yorkshire and Derbyshire.
The donations, made through the Prince of Wales Charitable Foundation, have been made to Foundation Derbyshire's flood relief fund and another from the South Yorkshire Community Foundation.
The donations have been matched by the Duke of Westminster.
Last month the Army was called in to help the relief effort in stricken towns and villages across northern England and the Midlands following weeks of saturating rain.
Charles spent two hours in the village chatting to many of the locals lining the streets and looking inside some of the badly damaged homes. Many of the villagers gathered outside the Old Butchers cafe which owners Louise and Claire Holling turned into a relief centre during worst of the flooding.
The royal visitor praised the pair when they turned up later at the village hall, serving refreshments for locals and dignitaries who had gathered to meet the prince.
As he left, Charles told the crowds: "I hope you've been in and tried those cakes. They're amazing those two, aren't they?"
Charles also met Angie and Scott Godfrey, who run the Hare & Hounds pub, which was another focus for the community during the deluge. Mr and Mrs Godfrey made sure stranded residents were fed by sending round hot meals on boats.
Mr Godfrey said to Charles outside the pub: "We were just going to get you a pint when you got here. You might have needed one by this time."
The prince replied "I do" and went inside for a quick sip of a half of bitter.
Charles also chatted to volunteers in St Cuthbert's Church, which is continuing to act as a hub for donations for those hit by the flooding.
He left Fishlake for a private visit to flood-affected farmers in Derbyshire.
Doncaster Council said 970 homes and businesses in the town were affected.
One of the worst-affected areas was Fishlake, where business owner Pam Webb's tears became an enduring image of the misery caused.
She learned that the insurance for her Truffle Lodge luxury spa did not cover flooding and last week she said: "There are people who have lived in this village all their lives who, with respect, are in their 80s and their 90s, and are looking at not being able to be back in their properties for possibly 12 to 18 months."
He was also asked about the health of Prince Philip, who has been in hospital receiving treatment in recent days.
"He's being looked after very well in hospital," Charles replied after being asked about his father's health by a reporter. "At the moment that's all we know."
During the visit, a woman in Fishlake asked Charles: "Sir, how is your father?"
He replied: "Alright. When you get to that age things don't work so well."