Sample collection methods frequently involve different degrees of effort in both field data collection and taxonomic resolution. The choice of a sample collection method is not only an essential part of designing field work, but can influence a site’s apparent status and thus the management and protection it receives. To investigate the effects of different sampling protocols on species composition and biological assessment metrics using macroinvertebrate assemblages, we examined the relationship between a typical rapid assessment approach involving low effort sampling (LES) and a more thorough and effort intensive collection method (high effort sampling, HES). Our results show that all indicator metrics had strong correlations within and among sample collection methods, whereas mean taxa numbers were significantly different between LES and HES sampling methods. Regression Models were used in the assessment process to assign standardized impairment status to each site. Assessment status of a site was the same for the two collection methods. However, models using HES data had higher R² and F-ratios than those using LES data. This comparison of collection methods could be used to understand accuracy and efficiency of different methods and to help design more appropriate sample collection methods.