Pollution was a method of inserting toxic or otherwise non-native materials into an eco-system.
Spock was able to confirm the arrival of the HMS Bounty in the late 20th century due to the high pollution content of the atmosphere. (Star Trek IV: The Voyage Home)
The Tagrans of Tagra IV requested assistance from the United Federation of Planets to help repair the ecological damage to their homeworld caused by pollution. (TNG: "True Q")
The technologically advanced race of Ledos was found to be polluting the area of a more primitive species that was their genetic ancestors, the Ventu. (VOY: "Natural Law")
The Malons built an entire industry devoted to the disposal of industrial byproducts such as antimatter waste. This hazardous waste was dumped into open space. (VOY: "Night")