I've been visiting the St. Lawrence river downstream of the Great Lakes since the 1970s. My mother grew up in the era before the Saint Lawrence Seaway was established in the 50s, which made the river navigable by larger ships (although not container ships) below the Thousand Islands to Montreal and the Gulf of St. Lawrence, opening up the Great Lakes to international shipping and trade.
The river used to be filthy. Lots of industry on the U.S. and Canadian sides and in the Great Lakes dumped all kinds of untreated waste into the ecosystem. I also remember a major oil slick which I believe was caused by a maritime accident. This was before the advent of better navigation technology and environmental protection laws.
The water may have become cleaner over time, but I noticed that by the early 2000s, the types of fish that I had caught off the dock by the dozens as a child in the 70s and 80s -- perch, sunfish, bass -- were becoming extremely rare. Ten years later, these shore species had all but disappeared except for a few bays and harbors.
The disappearance of these fish coincided with the appearance of the zebra mussel. The lore told here is that the zebra mussels were carried over by Ukrainian freighters in the 1990s (similar to the story in TFA). But other new species have appeared on the river, too -- cormorants, carp, and Canadian geese are very visible now, and they weren't in the past.
We also seem to have more extreme variations in water levels, with flooding this year and in 2017, and very low levels in other years. Surely that impacts water temperature and breeding conditions for some aquatic species.
I think some people blamed the zebra mussels and the cormorants for the disappearance of many species of fish, but I think there's a larger story taking place, with many factors contributing to changes in the ecosystem.