E. Any hazardous waste the mussels remove from chemical-plant discharge will remain in the mussels, if they do not transform it, and they then must be regarded as hazardous waste.

It looks like your confusion stems from assigning the "if they do not transform it" bit to the final clause of the sentence. I did the same thing upon my first reading. But it makes more sense to associate that middle bit with the first clause. This is because of the sneaky little "and... then" breaking apart the AC.

Another way to read this AC would be: "If they [the mussels] do not transform it, any hazardous waste the mussels remove from chemical plant discharge will remain in the mussels,............ and they then must be regarded as hazardous waste."

The rephrased AC makes some intuitive sense. Obviously, hazardous waste, if not transformed, is still hazardous waste. Even if it's just hanging out inside a mussel. And yeah, mussels full of hazardous waste should probably be regarded as hazardous waste themselves.

How do we know the hazardous waste will go into the mussels?

Check out this premise from the stimulus: "Since the mussels feed voraciously on algae... bags of zebra mussels... significantly improve water quality, even removing some hazardous waste." In other words, the mussels remove the waste because they eat the algae. And per the almighty question stem, this part must be true.

[W]e must accept the first clause of the sentence, which I don't think we currently have enough support in the passage to make.

Ok, so, taking a look at the first clause: "Any hazardous waste the mussels remove from chemical-plant discharge will remain in the mussels..."

Does the passage support this idea?

Kinda, yeah! We know the mussels remove some waste. That part is explicitly stated. If the mussels were to then release the hazardous waste, untransformed, back into the water, they wouldn't really be doing a good job of removing waste, would they?

Sure, so the mussels remove "some" of the waste. But what if they excrete a little of what they ate back into the water? That way the waste is still mostly, or perhaps temporarily, removed, the stimulus isn't violated per se, and AC E wouldn't seem so strong.

You're right. We kinda have to assume that that doesn't happen. But there's good reason for doing so. Simply put, the LSAT means what it means. In other words, each word is chosen carefully, and should be taken seriously. When the LSAT overlords wrote "even removing some hazardous waste," they meant removing. If the removal was temporary, they likely would have said so somehow. I catch myself making arguments like this one--arguments that turn on questioning the face value of a given word--all the time. Very very rarely do these arguments lead to the correct AC.

As for AC D, do we know that the algae clogs the pipes? Sure, the mussels can --and do-- clog the pipes, which part of the reason why they suck. But in order for D to make sense, we have to assume that, were it not for the mussels, the algae would be clogging the pipes.

That notion isn't mentioned in the stimulus... Is that a safe assumption to make? Maybe, I guess it depends on how much you know about algae. But, regardless, which of our above assumptions is easier to swallow? Assuming that algae can and would clog the pipes were it not for the mussels? Or assuming that when the LSAT writers said "removing" they deceptively meant "removing temporarily?"

The LSAT writers are sneaky to be sure, but liars and deceivers they are not.

I'd recommend investing in Score Preview. If you get your exam back and the score dropped, you can delete the lower score to instead show a cancellation. Law schools will take at least minor note of a score decrease, but will more or less overlook a cancellation.

As am I.