Cover = algae

If it was just dull/cloudy then I can imagine debris getting blown in that takes a while to clear via filtration, but unless you've got lots of greenish pollen (and it's usually more yellow than green) then I'm not sure where the color is coming from. I see that your waterline is blue, but is the fiberglass blue all the way down to the bottom of the pool? If so, then perhaps the green is yellow+blue (cyan, actually) so maybe the water isn't really green but is yellow which looks green against the blue pool surface. Yellow could be pollen or it could be iron, but since your pH didn't climb a lot I don't think it's metals. If you found that the color came with higher pH and went away with lower pH, then I'd suspect metals. At this point, it sounds like it might be pollen instead.
 
Thank you for your analysis.
Yes the fiberglass is blue all the way down.
It would make sense to me if it where pollen or even discoloration from the gum tree leaves constantly falling in.

The cover is back on now at night to try and keep it clean.

I'm going to periodically turn the in floor cleaning system on and off over the next few days and see if it is having any significant effect on the water colour. It may be just stirring up all the fine particles and causing my pool to look worse than it actually is.

Unfortunately I can't vacuum to wast as my pool wasn't fitted with those valve attachments. So my choices are to either suck it up with a manual vacuum attachment which sends all the dirt straight into the filter. Or use the in floor cleaner which sends it all through water and makes it look dirty.
 
Thanks. It's always good to get to the bottom of these things. Hopefully with the cover staying on you'll avoid getting pollen in the pool. You might notice it on the cover itself if it sticks there (might just get blown away). You might also consider using skimmer socks when your cover is off since they can often collect pollen before it gets waterlogged and sinks into the water. On the other hand, without the skimmer socks I'd expect the pollen to get caught in the filter so the water murkiness must mean that the pollen doesn't stay on the surface long. Perhaps the cover prevents it from moving to the skimmer so it's on the surface and then you cover it and it just gets waterlogged and sinks to cloud/color the water.
 
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