Andy, that is no small question! Probably all of our Yukon Hydro infrastructure would be considered "small scale" to the rest of the world, having a population of only 32,000, and a total hydro production of 75 MW. So it depends upon your definition of small! The application process here is two fold, first complete an environmental assessment through YESAB (Yukon Environmental and Socio-Economic Assessment Board), and then apply for the regulatory permits required, which could be lengthy, but would include a water licence from the Yukon Water Board (a quasi-judicial board established under the UFA - Yukon First Nation Umbrella Final Agreement), a Fisheries Authorization from the Federal Department of Fisheries and Oceans, a Yukon Land Use permit for any associated Land based activities, and so on, depending on the activities proposed. A good place to get an idea is from the water board website at
http://www.yukonwaterboard.ca/forms_info.htm#power , and check the info sheet. Or go to a recent licence at
http://www.yukonwaterboard.ca/licences.htm#hydro , and check out the licence and the reasons for decision. This is for Yukon. For the rest of the country, I believe that under section 91 of the constitution act, administration of water rights was assigned to provincial jurisdiction. Yukon, being a territory, just devolved authority for our land and water from the federal government 10 years ago or so.
I hope this leads you to the answer to your question!