"There are several lakes within Algonquin, every one I checked had the Mercury code."
A reason why there are possibly toxic mercury levels in APP fishes is the low pH of the lakes... the lower the pH, the greater the mercury uptake in the food chain. Lakes in limestone bedrock won't be affected much since the calcium-bearing limestone buffers the water and limits acidification, keeping pH higher. Most APP lakes are typical shield lakes without much calcium buffering capacity so pH can be low resulting in acid lakes.
The bigger-picture trend isn't good as you might have gathered from the news reports recently... decalcification of shield lake watersheds from acid rain is reducing buffering capacity and logging further decalcifies watersheds by removing calcium-bearing wood biomass where in the natural condition, the trees would fall and decay into the ground, returning calcium to the watershed and waterbodies
Resolving the effects of the rail bed from the bigger-picture decalcification isn't something I'd want to make a decision on in government... IIRC, both government and CNR have stated that they don't own that land and so aren't responsible for cleaning it up. One way to decide if rail bed remediation money would be spent wisely is to judge whether the rail bed remediation would actually result in any measurable improvement in toxin levels relative to the ongoing, bigger-picture decalcification and acidification trend. Not easy to do, probably, and needs money, which most likely isn't available at the moment.