This study evaluated results obtained from two artificial substrate sampling methods for generating community bioassessment data in potentially contaminated non-wadeable streams.  The methods involved placing co-located Hester-Dendy (HD) artificial substrate samplers in a stream with low flow and fine-grained sediments.  The first method was a standard protocol in which HDs were suspended in the water column just below the water surface (“top-set”).  The second method was an experimental protocol in which HDs were placed near the bottom substrate (“bottom-set”).  Data obtained from both methods were used to calculate Invertebrate Community Index (ICI) scores.  Results indicated consistently higher ICI scores for top-set HDs versus bottom-set HDs in this stream.  However, a study in a stream in a neighboring watershed with different physical characteristics (high flow and coarse-grained sediments) produced opposite results (higher ICI scores for bottom-set HDs).  For both top- and bottom-set HDs, ICI results declined with decreasing habitat quality and did not appear to be related to low-level contaminant concentrations.  These results demonstrate the influence of flow and sediment grain size on HD sample results, and that these factors should be considered when selecting sampling locations and methods for bioassessments in non-wadeable streams.