The Andes Amazon (AA) region of Peru supports a diverse aquatic macroinvertebrate  fauna for use in water quality assessment.  We collected 204 taxa (mostly genera) at12 sites ranging from conserved (pristine) to highly polluted in the Madre de Dios watershed.  Beta diversity was high with 102 taxa being found at only 1 or 2 sites.  The fauna differed significantly from previously studied streams in Costa Rica (CR) because certain dominant insect families in AA (e.g., leptophlebiid mayflies, libellulid and gomphid dragonflies) are not dominant the dominant mayflies and odonates in CR. Richness (number of taxa identified) was greatest for the insect orders Diptera [71–with 61 chironomids, followed by Coleoptera (27), Odonata (25), Trichoptera (24), and Ephemeroptera  (23)]. Total taxon (TT) and mayfly-stonefly-caddisfly (EPT) richness per site was generally highest in conserved streams and gradually declined with increased pollution (e.g., max/min was 99/13 for TT and 29/0 for EPT). Chemical analyses indicate pollutants ranged among sites from toxic chemicals (rural) to human waste (urban). Streams containing four out of five of the following aquatic macroinvertebrate groups [crabs (Grapsidae), mayflies (Campylocia), stoneflies (Anacroneuria), and two caddisflies (Phylloicus, Triplectides) always drained watersheds with significant levels of intact forest but limited pollutants.