I have just taken a couple more pictures (excuse the untidy house) from the stairs. As you can see it's an open plan area that isn't that big but very high ceilings also in wood (Macrocarpa) with dark wooden beams. The house is surrounded by bush so quite a dark house. I initially considered a darker wood similar to the beams but not sure if that will make the house appear smaller / darker...I'm really not sure what to do!?!?!? Thanks

You have "wear through" which is when the finish is pierced and the wood is exposed to the elements. The dark areas are where dirk/water/mud have stained the floor. It is possible to get this out... but probably not all the way. A floor that has wear through needs to be sanded right down, stained (if you wish) and then refinished. Patching can occur...but it is almost always a waste of time because the "look" can be very different from the original sitting right next to it. I don't recommend it for your situation. The second photo shows the deep scratching. Ideally, you would have had your floors looked after BEFORE wear-through occurs. There are some "regular" scratches to the Left in photo 2. You can see it is visible...but no discolouration....THAT is where you draw the line. The darker "wear through" to the Right in photo 2 = too late = full sand and refinish. If you catch it BEFORE wear-through, you can do a "buff and coat". This is a light sanding with a few coats of high end finish over top. The buff and coat is roughly half the price (in Canada at least) as a full sand/refinish. For this reason it is important to catch the floors before you get to this level of scratching.. That being said, you now get to pick some stains (test patch, test patch, test patch). The first photo shows two different woods...you could ask to see if the lighter would could be matched to the darker wood (lots of testing to achieve this). It won't be pefect...but then again you wouldn't have used reclaimed building materials if you were after "perfect". The match can lessen the colour variation to a more manageable (design wise) level. As for "good for dogs" - natural colour of wood = best colour for scratches. A lower gloss (like a satin) can help. You can ask for the "best" finish with scratch resistance that comes in a can. You will pay a premium for it...but it could/should save you thousands of dollars over the long run. A highend, scratch resistant finish means you can get away with the cheaper buff and coats (every 7-12 years...or so) and be able to retain the original (expensive) finish for the full 25 years. The other thing to note: dogs claws require trimming 2-4 PER MONTH when working with hardwoods. This is what the hardwood flooring refers to as "routine" trimming. Some of my clients thought "2-3 PER YEAR" was "routine". I laughed. You have heavy, high energy, powerful dogs. A single lab can cause some damage over time. Two labs can do a number on a floor. Three labs and you have a very short lived hardwood finish. You have 7. I would find the most expensive, scratch resistant finish available in Australia. I would have the maximum amount of finished put your floors (you will pay extra) it and I would budget for a "buff and coat" every 5-7 years.

Thanks for all the great ideas everyone and sorry I didn't explain the polycarbonate a bit better :) This is along the lines of what we'll be using... http://www.psp.co.nz/building-brands/corrugated-sheeting/suntuf-polycarbonate The area is an absolute sun trap and we're hoping to use it as an extension to our living space, especially on rainy days! I've just sent my husband out to get a few pots of different stains for is to try - darkest brown (cedar) and a lighter brown (rustic oak) both by Cabots + the black we already have. Hopefully we can decide between one of those! I probably should have mentioned we will have black aluminium pool fencing running along the top of the second retaining wall - so the real question is do we keep everything black (pool fencing, horizontal fence, retaining walls and pergola) or do we go with a dark (or even light) brown for the pergola and retaining walls.... We just keep going around in circles at the moment. Decisions, decisions! Thanks again :)

Alternatively, if you just want to get the water marks out of the wood: Set an iron to warm (not hot) and allow it to heat. Lay a cotton napkin or tee shirt over the water stain. Iron the stain through the cloth for 5-10 seconds, then remove the heat for 20-30 seconds. Repeat as necessary, buffing lightly with the cloth after every 2-3 heat cycles. A hair dryer may used instead of the iron. Set it to medium heat and hold 2-4 inches from the stain. Buff the stain with the napkin or tee shirt as you heat the wood.