Pond water clarity is a subject close to my heart, since my clubs pond went pea green and remained that way last year.
Basically it boils down to one thing- too much nutriment in the water, which enables algae to flourish resulting in murky water.
This can be through rotting vegetation i.e. leaves in the bottom, Canadian geese poop etc.
In effect the pond becomes an open sewer.
If the water only has a small amount of nutriment, then it will likely go a bit murky for a while, until the algae saps all the nutriment from the water, whereupon the algae dies of starvation and sinks to the bottom.
There are only two solutions to this.
Regular cleaning of the pond, chemical treatment (biological or industrial) and/or filtration.
Natural ponds or springs don't suffer from this, because they have a natural exchange of water, so the water nutriment never rises to critical levels. Where natural ponds occur, and are largely stagnant, you will usually find that lots of water plants start to grow in the pond i.e. water lillies, reeds etc. which leach the nutriment from the water.
Unfortunately, this doesn't make for a very navigable pond!