The water being crystal clear looks cool, but it's an ecological disaster for larger fish in the food chain that depend on the turbidity of the water for ambushing smaller fish.
There are almost no "native" species left in any of the lakes (excluding superior).
If you want sustainable native great lakes ecology you need to cut them off from the oceans, re-reverse the flow of the Chicago and do a one-off massive trout and other native fish stocking. None of that is ever going to happen so until then we can keep experimenting with ecology and in that case Zebra muscles is much better than massive population booms and busts of alewives or other invasive fish species (Salmon were originally introduced to help keep the alewife population down)
This includes everything from walleye, lake trout, and perch all the way down to daphnia and diatoms.
The problems for native species in the Great Lakes has been driven by the introduction of zebra mussels, quagga mussels, the round goby, and spiny water flea (bythotrephes) for native food sources.
These new species have interrupted the food chain and therefore the reproductive fitness for many native species which further decimates the natural Great Lakes ecosystem.
1) Clearer water means that light reaches deeper. Potentially allowing more aquatic plants to grow over huge new areas. Providing new habitat, food sources and shelter for fish.
2) Zebra mussels might trap some chemicals like PCBs. And accumulate them in their shells. Once the mussel dies, they fall to the bottom, and might permanently lock up them up into the sediment.
But this isn't necessarily a desaster, not all lakes are equal in their conditions for various species. This might just be what the lakes looked like for the longest time.
Btw., there are large fish hunting smaller ones in clear water. Most extreme example are sharks.