While it is true that choice E lacks the serial ("Oxford") comma between the parallel items in the list, in my experience the GMAT will never make such a fine point the SOLE reason for eliminating an answer choice. There must be a more substantial reason for eliminating the answer choice. Here the reason is that the participles (permeating ... washing ... replacing) grammatically modify NOT groundwater but the subject of the sentence, bone. But the sentence's logic demands that these participles modify groundwater, so the result is nonsensical.

Here's a similar example where the connection between the participle and the subject modified is clearer: The soccer team has a complicated relationship with its fans, encouraging their support but fearing their fanaticism. The participles encouraging and fearing clearly modify the subject soccer team, not the object fans.

Now take the following example: The forager walked through a forest resounding with the calls of songbirds. The participle resounding modifies the object forest, both logically and grammatically. That's because there is no comma between forest and resounding. If this sentence had a comma after forest - The forager walked through a forest, resounding with the calls of songbirds - the result would be nonsense, because then resounding would have to modify the subject, the hunter.