The form of mercury in fish is especially toxic to humans. It's in an organic form called methyl mercury. The methyl form is produced in environments rich in organic materials. Anaerobic bacteria, who thrive without oxygen in sediments, scavenge elemental mercury and excrete it as methyl mercury. Some plants also scavenge mercury.
Fish get it by eating critters that are lower on the food web.
Because mercury has been used in so many industries and mines, it seems to be ubiquitous. There are no coal-burning power plants upwind of Tahoe. And there were no mines in the basin. They found mercury in Tahoe sediments. Sediments in the bottoms of lakes and ponds contain historical records of things that erode or fall into the water.