I've compiled some resources regarding rules that govern high altitude balloon flights as well UAV systems for amateurs in Canada. Based on my own experience, I would advise close communication with Transport Canada (the regulatory body; kind of like the FAA in the US).
This link pertains to how UAVs are regulated in Canada. Essentially, if your UAV is less than 35kg (usually the case) is for recreational purposes, you should be fine. However, if this is not the case, then you must apply for a Special Flight Operations Certificate. In our case, we propsed this as a University project, so we needed to apply for an SFOC. The laws are outdated, but there is essentially one person for the whole country who oversees such operations. I will mention that you probably should coordinate with Transport Canada if you are flying a UAV at near-space altitudes. This is because you should coordinate with NAVCAN, in order to limit the risk of danger to full scale flying and ground populations. Flying at that alittuide is experimental at this point, and many things can go wrong. So it is necessary to exercise reasonable caution when doing something like this.
Balloons are less of a hassle. If your balloon is less than 115 cubic feet, you need only coordinate with your local flight center and post NOTAMs as necessary. If your balloon is larger (usually the case for High altitude and heavier payloads, such as a UAV), then you need approval. I've attached the information needed for such cases. It is not difficult, but there are some things you may need to modify to your system to comply. Consider an excerpt from an email I've received from a fellow at Transport Canada:
As we discussed on the telephone today your proposed class project of a
balloon flight using a 220 cubic foot balloon to lift your glider will
require an authorization from Transport Canada. A large unmanned balloon
is defined as having a gas-carrying capacity of more than 115 cubic
feet. In order to maintain an acceptable level of aviation safety with
respect to your proposed flight, you will need to comply with Section I
- Balloon Launch Restrictions and Section II - Operational Procedures
contained in the attached PDF file.
The request for flight approval should be in the form of a letter or
e-mail. This needs to address the balloon and payload composition,
materials, colours, launch site and time, duration of flight, planned
maximum altitude, means of tracking (radar reflective or transponder
equipped), means of termination, payload and balloon tracking on
descent, and any other information that may be applicable.