Colony for not breeding times in the summer when shade is enough and hutches for breeding season so you know who is related to who. Knowing the traits of your does is important, handling bunnies helps with plenty of things including care and possible sale as a pet.
Either get a permit for building rabbit housing the size you want or work with what you have and adapt housing to the season. Dry feet (and liquid water) is baseline for landbased livestock.
One of my does comes from a breeder who has all does in a big outside pen in the summer when she is not breeding. Winter/breeding season they have their own hutches in the shed/barn. Be flexible and adapt housing to weather and what you have.
For water as in rain, the first rule is : it finds/seeks the lowest point i.e. tunnels, holes and so on. That makes going underground a bad idea for solutions. You could try building small hills in your colony (pipes and everything), but i suspect you'll need to pave everything first (including under the hills) so they can only dig into the side of a hill, not down after all. Note on that, not all soils are suitable for unsupported tunnels, they may very well collapse due to weight (bunny or human) combined with weather.
Colonies i see are either indoors or in dry climates. Not everything translates well or wholesale to another area.
I would sit down with a pot of tea/coffe/whatever and write down your goals for breeding (closed herd just buy in new bucks every so often, care (who has to/can care for your animals if you (or worse your family) can not? And what works best for each, add regulations, feed costs and local concerns (soil type, pests attracted to feed/manure, neighbours complaining about smells and so on)
Note that while animal wellfare laws may not be well defined getting inspection send to you from neighbours (or workmen for maintenance and so on) means first impressions are everything. Place looks neat, animals happy, active and so on gives you benefit of the doubt and inspector more likely to label the complaint a misunderstanding or friction between people rather than abuse/neglect.
