Answering the challenge
You both make valid points, Ddugger and Omb, which brings me back to wondering why the scientists embarked on this research in the first place. Of all the things to test for, I'd like to have been there (or maybe not!) when some PhD said "I know, let's analyze the Pacific for caffeine." Huh? What's next, dredging the Mississippi for saccharin?
But now that they've done it, and to address your main point: The researchers seem to regard beverage and food as the main source of the caffeine. They also say that pharmaceuticals released some of the stuff. They RULE OUT natural sources. From the press release (link in the story): "Caffeine is found in many food and beverage products as well as some pharmaceuticals, and caffeine in waterways is directly related to human activity. Although many plant species produce caffeine, there are no natural sources of the substance in the Pacific Northwest. The presence of caffeine in ocean water may also signal additional pollution such as pesticides and pharmaceuticals."
After all this, I'm still sticking with 3 morning cups of strong, black and preferably Italian roast. I'll do my best to leave it out of the ocean. Might be tough, as I live on an Atlantic island.