A curious tale! Not least because the writer has no compunctions about referring to squid as fish. While the group "fish" is by no means taxonomically rigorous, and comprises creatures as diverse as hagfish, sharks, and coealacanths, the one thing all fish have in common is that they're vertebrates. Squid are squarely in the invertebrate camp, and therefore excluded from the fish club.

Linguistic quibbles aside, this really is strange:
EXPERTS have no answers on what has caused the death of thousands of squid in the River Derwent this week. Dead and dying arrowhead squid have been washed ashore or spotted floating on the water at Austins Ferry and Berriedale since Tuesday.
Arrowhead or arrow squid, also called (by those in the Linnean know) Nototodarus gouldi, are abundant all around the south of Australia, including Tasmania. But, like all other cephalopods, they are solely saltwater animals. So the fact that they were found dead in a river at first seemed like a no-brainer to me: Duh, rivers are freshwater, squid can't surivive that.

But then I checked on the Derwent River, and learned that in the area around Hobart, where the squid were found, it's actually an estuary, and probably quite salty. So what went wrong? The EPA director said:
"It is possible that these fish [sic] have been caught in low-salinity water following the high stormwater discharges over the weekend."
That seems pretty straightforward. But then the people who've lived in the area forever claim they've never seen anything like it before (and there have likely been plenty of storms before). So is the mass squid mortality a sign of the end times?

Probably not. Psychology says that we humans are fabulously good at forgetting, and forgetting that we've forgotten, so it's quite possible that those people have seen something like it before. Or maybe they haven't seen it, but it has happened, and they didn't notice it because there was something else in the news that day, or they were busy celebrating a birthday, or what have you.

It was probably just a lot of unlucky squid that happened to be in the harbor when a surge of freshwater poured in.