Environment Canada says the Guelph area and Waterloo Region could see some heavy rain Thursday night and into Friday.
The agency issued a special weather statement that also covers Wellington County and most of southern Ontario.
The weather office is warning of isolated thunderstorms and rainfall amounts in the 20 to 50 millimetre range.
The rain should taper off by noon on Friday.
But Environment Canada said strong winds gusting up to 80 kilometres per hour are in store for Friday afternoon.