The determinination of an adequate collection protocol for protists is critical in the examination of their distribution and composition in temperate headwater streams. The objective of this study was to test which sampling design/sample gear combination would yield a cost-effective, site-representative protist assemblage. Defining parameters included greatest taxa richness, abundance, morphological diversity, taxa overlap, and cell-size diversity. Two sample designs (i.e., transect and mesohabitat design) and two sample gears (i.e., benthic grab sample, and a colonizing device [polyurethane foam unit, PFU]) were tested in three 100-m reaches representing the predominant environmental conditions (i.e., fragmented woodlots and agriculture) in the study area. A two-way ANOVA was used to evaluate abundance taxa richness and abundance of the protist assemblage (fixed effects) across the three reaches (random effects). The mesohabitat sampling design had the highest mean in both taxa richness (n = 72, P = 0.0012) and abundance (n = 72, P = 0.0004). The highest mean was reported with the benthic grab sampler (39.89 ± 1.1) in the abundance count only (n = 72, P \ 0.0001). There was no difference in the design and gear interaction. Morphological diversity, cell-size diversity and percent taxa overlap between sampling design/sample gear combinations also were examined. A higher taxa overlap of the top 10% most abundant taxa was observed with the benthic grab sampler (43-100%) versus the PFU (25-69%); however, the greatest morphological and cell-size diversity was produced by the transect design/PFU combination. We conclude a ''hybrid'' of the two sample designs will account for ''patchy'' distributional patterns of protists and use of the PFU, because of the highest yield in morphological and cell-size diversity, will provide the most costeffective, site-representative protist assemblage in temperate headwater streams.