Well, the technology was not intended to pollute of course, but since the mining facility only halfway works now, there is nothing to harvest the little trickles of oil that spill out from parts of the machine. Now think, would this happening over centuries eventually begin to pollute the water? Yes, of course it would. My theory is that the Zoras managed to hold off the oil from spreading by closing it off with an underwater cemented wall. A giant particle-eating fish could have also been turned upon the facility to actually eat the pollutants in the water, and they planned for the poor creature then to die. However, eating all those pollutants (not just oil, but things like acid from the seawater combining with the corroding machinery) has given this fish sustained life, however, this was achieved by mutation of the fish's molecules through eating the otherwise toxic pollutants. Now, yes, there are pollutants at the bottom of the Selepria Sea, as the facility was abandoned after the Zoras had to migrate elsewhere during the 2 year storm, when the waters of Selepria were nigh impossible to navigate, even for Zoras, for a full two years.
This left the machinery the mining facility was composed of damaged, and supposedly inactive. Saying that there is an abandoned mining facility that doesn't pollute the water is highly unlikely, and I devised this scenario so it would make more sense.
