I called a representative from the Canadian Border Services agency about this rental car
policy question. He said that for you, bringing a rental car into Canada from the United States is no problem at all - the determining factor on being able to take a rental car across the border and into Canada is your country of residence rather than your citizenship status.
Basically, Canadian Law prevents a Canadian "resident" from bringing a US owned car into Canada.
He confirmed that in your case, although you are a Canadian citizen, you would be considered a US resident NOT a Canadian resident and therefore you will have no issue with being able to transport your rental car from the US to Canada and back.
You can find information about many aspects of crossing the Canadian Border (travel tips, entry requirements, prohibited and restricted goods, etc )at
You must make sure that you have permission from the car rental company you're renting from to take the rental car into Canada and make sure to have your rental agreement as well as any documentation required by border patrol.
Pages from this site, relating to this topic:
Taking a rental car into Canada