Wow, Paul, that's a bad one.
So you are off the grid. So you're the power system designer, and electrical inspector??
I would look seriously at a very good ground system. Multiple ground rods, maybe bonded with a large conductor all around the perimeter of the building.
What is your layout like? What is the soil like? What is the terrain like? How far away is your MicroHydro? Your Solar panels?
Based on my experiences with big pulses coming in from long wire runs like 100 feet to my submerged water pump and 200 feet to Ski Lights, you need to think about transient suppressors like large MOVs, and Fuses (remember fuses?) near the point where long lines enter the house. Lightning blows the fuses in the box to my water pump about once a year. The circuit breaker never trips. These are old screw-in fuses but they protect me.
I have regular USA power (115/230V single phase, grounded neutral) and I have two hockey-puck size MOVs directly on the service panel from the power rails the breakers plug on to, to GROUND which is extensive.
I designed (and fixed...) Broadcast Transmitter and Tower installations for years, then I went to IBM and worked on micron-sized stuff.
There's a good subject here; maybe we should start a thread. Arduinos etal will be connected to stuff like 50 foot cables with DS18B20 temperature sensors on the end. Sounds like an antenna / lightning pulse receiver to me.
Stuff is known about this. One of my kids designs Wind Energy Loggers (http://nrgsystems.com) which have lots of sensors on a tower and logger electronics with 2 or 3 ATMEL controller chips in them. He has extensive protection components in these. I'll try to pull him into a discussion.
Tell us more about your situation.