Google for the term bioaccumulation. Your body, for example, has serious problems with bioaccumulating radioactive iodine and strontium and a couple other elements. The Japanese plan was to plant fungi that looooove eating cesium and accumulating it in their fungus flesh (well, maybe it wasn't cesium, but you get the idea). Then you scrape up the radioactive, dying fungus into waste barrels and plant some more, and eventually all the bioaccumulative element is in barrels instead of dirt.
There are of course minor engineering issues like how the heck you gather the bioaccumulated plant matter without using humans who will contaminate themselves and die and/or make a bigger mess than just leaving it alone.
There is also a little engineering problem with scale... say you had a major DDT spill which thins poultry eggs killing off wild birds. Well, you could put an industrial poultry fryer farm over the DDT spill and bury the DDT contaminated eggs in the bottom of the ocean, or maybe incinerate them or something to provide cogeneration heat and electricity to run the plant... yeah... it would just take a trillion birds a billion years to clean up a major spill. Other than that minor scaling engineering problem...
(1) Bombarding with neutrons or high energy charged particles may change the amount of radioactivity. Also, positron-emitting nucleotides can have slightly faster halflife at very low temperatures. None of these methods are available for the fungi.