Anthropogenic salinization of freshwater is a global concern. In freshwater environments, elevated levels of major ions, measured as total dissolved solids (TDS) or specific conductance (SC), can cause adverse effects on aquatic ecosystem structure and function. In central Appalachia, eastern USA, studies largely rely on Rapid Bioassessment Protocols with semi-quantitative sampling to characterize benthic macroinvertebrate community response to increased salinity caused by surface coal mining. These protocols require subsampling procedures and identification of fixed numbers of individuals regardless of organism density, limiting measures of community structure. Quantitative sampling involves enumeration of all individuals collected within a defined area and typically includes larger sample sizes relative to semi-quantitative sampling, allowing expanded characterization of the benthic community. Working in central Appalachia, I evaluated quantitative and semi-quantitative methods for bioassessments in headwater streams salinized by coal mining during two time periods. I compared the two sampling methods for capability to detect SC-induced changes in the macroinvertebrate community. Quantitative sampling consistently produced higher estimates of taxonomic richness than corresponding semi-quantitative samples, and differences between sampling methods were found for community composition, functional feeding group, dominance, tolerance, and habit metrics. Quantitative methods were generally stronger predictors of benthic community-metric responses to SC and were more sensitive for detecting SC-induced changes in the macroinvertebrate community. Quantitative methods are advantageous compared to semi-quantitative sampling methods when characterizing benthic macroinvertebrate community structure because they provide more complete estimates of taxonomic richness and diversity and produce metrics that are stronger predictors of community response to elevated SC.