If there are real biohazards or chemical polutants then special equipment and procedures are called for.
Sorry Fred, the band mask doesn't cut it, you need at least a full helmet with dry suit and dry gloves, with double exhaust valves in the helmet. That is just for starters. Depending on the hazard it can get worse.
Divers working in the nuclear power plants wear special shell suits and nearly always the Desco air hat. The Desco gets the job because it is all metal so it doesn't trap any radioactive contaminates and it is a free flow hat so there is nearly zero chance of any water getting inside.
For chemical contaminates you have to make sure that your suit, suit seams, gloves, boots, helmet, neck dam, umbilical and anything else that will contact the water will withstand the chemical for the duration of the dive plus a safety factor.
In some cases the dry suits become a consumable item, being replaced after 45 minutes or so in the water. Can you say, "Expensive job?" I think you can.
For normal muck on a normal lake it is not so much a problem.
Watch out, some lakes have some nasty microscopic critters in them that will do bad things to you.
Getting into the muck at the bottom of Lake Appoka here in central Florida can get you some real nasties. ;-0
The worst lakes seem to be the ones that have been getting lots of fertalizer and pesticide runoff.