Not all, but most pollution comes from nearby agriculture-
Studies Confirm Presence, Severity of Pollution in US National Parks. Science Daily
The worst of the problems is pesticides.
Ralph Maughan
Dr. Ralph Maughan is professor emeritus of political science at Idaho State University. He has been a Western Watersheds Project Board Member off and on for many years, and also its President. For many years he produced Ralph Maughan's Wolf Report. He was a founder of the Greater Yellowstone Coalition. He and Jackie Johnson Maughan wrote three editions of "Hiking Idaho." He also wrote "Beyond the Tetons" and "Backpacking Wyoming's Teton and Washakie Wilderness." He created and is the administrator of The Wildlife News.
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I’m not surprised, given the proclivity of so many humans to traveling by mechanical means, not the two legs nature gave them. I’d be happiest to be able to put our cars behind us for just long enough to backpack a bunch of miles from the nearest road.
It’s absolutely no surprises at all that pesticides are the biggest culprit.
What other creature on the planet *poisons* its own food on purpose?
We really are insane. That is the cold hard truth.
Invasion of non-native species also tends to come locally from the outside if the Park. An exception to this can come to Parks that attract many vehicles from distant places.
Slightly off-topic but a good source of invasives in the southwest:
http://www.desertmuseum.org/invaders/