Remove brush and debris from the stream or creek where you have problems with black flies. The larvae require debris in the stream to hold onto in order to get food to develop. When you clear the debris you remove much of the habitat they need to grow to the adult stage.
Check with the local conservation department to make sure there is no local regulation against the use of BTI cakes, commonly called mosquito dunks, in the stream. You can find mosquito dunks in the pest control sections of many hardware and home improvement stores.
Put the mosquito dunk BTI cakes within 50-100 feet of each other in the stream, provided they are not banned in your area. Begin putting them out about three weeks before the beginning of black fly season in your area. Black fly season can vary dramatically depending on your location, so check with local authorities if you are not sure on the best time to start. Make sure to place the cakes in various locations throughout the stream so that all the water supply is treated. The cakes should take about four weeks to dissolve completely, but check every couple of weeks. When they are completely dissolved, re-apply cakes until black fly season is over.