Bundeenabuoy said..
I recently connected a new water pump. I then topped up the tank. When the water started to flow there was a slight momentary brown colour in it which quickly disappeared. It tastes fine, but I think I should pump all the water out.
My issue is: Will I damaged my new water pump running it for more than ten minutes at a time? or can I pump the whole tank out in one go?

How big is the tank?
100 litres would take a fair while to pump, I guess.

If it tastes fine couple of drop of water purifier would be all I would do.

Gray

Is there a way of releasing the water flow before it hits the pump?

Personally, having suffered a nasty case of Aeromonas hydrophila from an unidentified source (the only possible source was boat water tanks, even that being unlikely, but...), if you have doubts about contaminated water supply, empty it out and start afresh with some sterilising tabs.

I do a complete empty every 6months, pour copious quantities (say 10-15l) of vinegar into the tanks, let it sit for 24 hrs then flush until I can no longer taste vinegar.

When you check tank water in any building there's a natural build up of brown slime or sediment on the base. It's why the outlet is a few inches off the bottom and a drain plug below. I'd say the brown is exactly that sediment. Having said that, if there's particles, usually white, then that toilet cross connection has happened and it's time to detox the tank.

I recent installed a Jabsco pump and their specs say the pump can run dry for extended periods. So while it makes sense not to run it more than necessary like that, it probably won't damage it.
They also have a Jabsco Aqua filter which could be installed next to the pump. They come with a secondary replaceable filter priced around $100. Worth considering.
I emptied my water tank with only clear water flowing. I plan to use Aquatabs or a similar product when next I fill my tank.
Thanks for all the advice.

One thing to watch for if you're pumping out the crud from the bottom of your tank is clogging of the little screen filter that is built into some pumps. It's easy to remove and clean, but just as easily forgotten.

Good option for pure water is a 2 stage filter with 2nd stage at .5 micron to remove all flavour.