Documentation of biological responses to changing sediment and stream water quality conditions require repeated sampling over extended periods of time. Consequently, significant budgetary and personnel resources must be devoted to maintenance of biomonitoring networks. Alternative methods for monitoring biological responses that are more cost-effective than traditional benthic sampling approaches are of interest to agencies charged with measuring or managing water quality. In recent years we have refined an alternative approach for biomonitoring that relies upon collection of surface-floating pupal exuviae of Chironomidae to augment or replace benthic sampling. Our results indicate that collections of surface-floating pupal exuviae are more efficient at determining patterns of chironomid community composition in routine field sampling. Collections are easily standardized using time-effort approaches, show high statistical precision and require approximately one-third the time to process compared to benthic samples. Increased taxonomic resolution is generally achieved with pupal exuviae relative to benthic collections of larvae. Our collection protocol is described and sampling efficiency, efficacy and economy discussed.