Mercury
metal is heavy but mercury ions aren't. The amount of mercury in the water would depend on a number of factors such as the acidity of the water near mining activity, the amount used, temperature of the water, etc. If, as Blues Frog says, the gold is silver, that means that there is a huge amount if mercury present. I doubt, highly, that anywhere has that much mercury around. Not disturbing the sediment would help but the mercury that you have to worry about is the stuff that is dissolved.
But mercury would be the least of your worries in mining districts. There are, roughly, 20 heavy metals that cause problems in mining districts. Many are far more reactive and far easier to get into the water than mercury is. Arsenic, for example, forms salts readily and then can dissolve to fairly high concentrations making it more toxic than mercury which is less reactive and less soluble.
With a proper filter, biological hazards are easy to deal with...it's simply a matter of particles and filter size. Heavy metals can't be filtered out because the particles are far too small to filter. If you had a filter small enough to trap heavy metal salts, you couldn't pass water through it.
The rule of thumb I use is that if the waters have trout* in them...and/or fishermen trying to catch the fish...the stream is probably alright to filter from. If, on the other hand, the stream is rusty looking,
flowing out of an obvious mine or hasn't got trout in it, you might want to look for another source.
*I pick trout because trout are damned delicate. Catfish, carp and bass can tolerate much higher levels of nasties and still survive. If the waters have a healthy population of trout, the water is pretty good. The Arkansas River in Colorado, for example, has a very health trout population even with a small amount of mine drainage. Clear Creek below Central City/Black Hawk has almost no fish (and hasn't for years) because of mine drainage.