I need a creature that can survive in environments with elements like lead and mercury in many nutrition sources, and in some places making up part of the atmosphere.

I was thinking maybe it could have an organ with other elements that readily bind with the heavy metals, making them not toxic or detrimental. However, I'm not well versed enough in chemistry or biology to know if that makes sense.

Creatures that evolved in metal-rich environments would be immune

Evolution could take care of the toxicity problems. Metal toxicity is a characteristic of many different metals, and the root cause for why a metal is poisonous varies widely between metals. For example with arsenic:

Arsenic interferes with cellular longevity by allosteric inhibition of
an essential metabolic enzyme pyruvate dehydrogenase (PDH) complex,
which catalyzes the oxidation of pyruvate to acetyl-CoA by NAD+. With
the enzyme inhibited, the energy system of the cell is disrupted
resulting in cellular apoptosis. Biochemically, arsenic prevents use
of thiamine resulting in a clinical picture resembling thiamine
deficiency.

Arsenic interacts with specific enzymes in a specific way to disrupt them from doing their biological job. The solution is for organisms to evolve specific methods for resolving whatever biochemical problem the metal causes. For arsenic, an animal which evolved so that that allosteric sites on the PDH complex enzyme are not receptive to arsenic. The biochemical reaction chain is broken, and now arsenic is not any more problematic to us than eating iron (well...there may be other problems arsenic causes, this is just the one that kills you fastest).

Humans are immune to the metals common in the environment

In the Earth's biosystems, certain metals are present in certain quantities. These metals are needed for nutrition, iron, magnesium, potassium, etc. The amount of iron or aluminum, two common metals, found in organic matter will not poison an organism on Earth, since all organisms on Earth have had to deal with these common metals for billions of years.

If you planet has a different geo-chemistry, or different elemental abundances in the crust, the creatures of your planet, since the inception of life, will evolve a resistance to the metals commonly encountered. Therefore, you can assume that any creature on a heavy-metal-heavy planet would be immune to the commonly encountered heavy metals.

The creature’s small intestine has a magnetic lining that attracts heavy metals. It removes metals when the food is liquefied, for easy separation. The magnetic field can be created by magnetizing small chunks of iron using electric currents in nerve fibers.

I would start with the igaunas of Galapagos as a reasonable visual of what some creature plaqued by pesky heavy metals could look like. Constantly excreting the poison through the nose and skin.

Of course some metals in microscopic doses are necessary and tolerable. So yes the organ might work which picks up and filters the blood. But really the metal would mostly enter through skin and lungs. So those organs must feature some coating or ingenious enzyme that eats the metal, sends it to another special organ which turns it into energy or poison the animal could use as a defense. Also you could use a magnetic aura against the non-ferrous metal or an acid which dissolves it. And maybe that special organ could have a separate chamber which pools the ferrous metals and excretes them to be harvested by humans or other symbiotic creatures.

This feature of metal eating creatures might give them some supernatural abilities. Might even allow them to talk to each other telekinetically, or Have metal skin, poisonous concentrations of saliva, or a lot of other scientific uses.