Your concerns are more significant than some may think so. My only concern is to fill this "lagoon" with local fishes, catched in the nearby sea. I dont intent to bring some exotic species over here. Secondly the waters are not poluted, so there is not any change to pumb poluted wated into the tank. Also, I dont think that the sea has to be afraid of my actions, because if I manage to achieve the same environment to the tank as the sea, then there is no reason to add even one ml of toxic, chemical substance. If there is a way to have the fishes there, and to live without an external help then everything will be ok and I will proceed to completing my plan. If there is no way to mantain life there, without external help, then I am afraid that I have to leave the fishes in the sea. The magic word here is the interchanging of waters, which will hapen continuously, because there will be a 24/7/365 communication of the tank with the sea by a large pipe.
I dont know if it is gonna work, thus I would like more ideas. Do you think that there may be a chance for the creation of a suitable environment (O2, CO2, PH) by only allowing the tank to communicate realtime with the sea. I will try to put the tank deep enough in the soil in order to have the upper part of the tank at the same level as the sea, and thus no power will be need for the water that will come in and out of my tank.