Even the most common horse and house flies can transmit diseases. The horse and black fly can leave a very nasty bite. The black flies can be very persistent in their attacks. You can best protect yourself by avoiding travel during peak fly season, which can vary by region. Wearing insect repellent and covering exposed skin will help reduce the amount of bites received.
We have a niece (Kit) that performed a school project while vacationing in Canada. It was determined after applying several different lotions during the summer environment that Hawaiian Tropic Sun Tan Oil performed the best against the black fly.