Assuming the process is something akin to the Groundwater Replenishment System in Orange County, CA, those shouldn't be a major problem. I'm too lazy to look up the treatment plant in this story, but I'd guess that the article leaves out a few steps in the treatment process, including some sort of advanced oxidation process. At the GWRS in CA, that would be a hydrogen peroxide / UV step that oxidizes the crap out of anything that might make its way through the RO process -- which isn't much, except for possibly neutrally charged, small molecules. Further, it if it's a well run wastewater collection system, there should be source control measures in place to minimize a lot of nasty stuff, like heavy metals and toxins, as that throws off advanced wastewater treatment processes as well.
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According to his own website, GRRM hasn't even finished it yet. I'm not believing anything about this book until I can buy it.
My understanding was that there was a chance it might make things worse. If the mud didn't actually slow the leak, but was pushed out as fast as it was applied, there was the fear it might further damage the already broken valve. So, rather than a partially open valve somewhat checking the flow of oil, you'd have a fully open pipe.
Except, at least with the deal we got from So Cal Edison, we give them the right to shut off our air conditioner in exchange for a discount on our summer electric bill. I don't recall exactly how much of a discount on the energy they gave us, but considering that they never once actually killed our air con during the summer, I have no complaints whatsoever.