Mining Impacted Stream Reaches 
Abandoned mine impacted tributary on left, iron and aluminum precipitates, 
unpolluted tributary on the right
The most common water quality issues related to mining are low pH, high heavy metal concentrations, high fine sediment levels and dewatering of streams.  An example of how to evaluate the effects of historical mining projects on stream ecosystems and a good description of the effects of abandoned mine lands on stream invertebrate assemblages is available in a report of a project we began last year in the Gunnison River Watershed in southern Colorado: Mining impacts to aquatic invertebrates in Henson Creek, Colorado
Instream habitat High fine sediments loads are common.  Films of iron leaching bacteria may cover mineral substrates.
Aquatic invertebrate sampling equipment kick nets or Surber nets
Invertebrate assemblage members Ephemeroptera (mayflies) appear to be most adversely effected by low pH and heavy metals. 
Diptera: Chironomidae may dominate