Alright, could it be possible that the K.A.C.C and Area 69 are responsible behind the Water Pollution, they are both connected because in real life Area 51 is an Air base, and K.A.C.C is an aviation fuel depot. K.A.C.C is the closest base to the Pipes north of LV, the US Air Force also appears in the mission N.O.E, trying to shoot down what appears to be liquid in green canisters, this could be Green Goo, Toreno even says its "highly dangerous material". K.A.C.C is linked with the Water Pollution pipes, and sometimes the water glows Green, there's also green pipes inside Area 69. One final piece is that during the mission in which Carl steals the Goo, the train appears to be going from K.A.C.C to somewhere else.
Could the Goo possibly be Jetpack fuel? Comment on this below.
Thanks to Jim and Indep for helping me out.