Intermittent, headwater streams constitute the bulk of most drainage networks and present unique habitat challenges to resident fauna. Intermittent streams typically progress through flowing, interstitial, pooled, and dry stages annually depending on local climates.  The objective of this study was to describe macroinvertebrate communities associated with different hydrologic phases of intermittent, headwater streams in South Dakota’s Northern Glaciated Plains ecoregion. Twenty study streams were identified using the USGS National Hydrography Dataset (watershed area=1-6 km²) and determined to be minimally disturbed based on watershed condition scores generated from the US EPA ATtILA interface.  Sites were sampled monthly from April through August, 2008. Twenty five percent of streams sampled remained flowing or interstitial, 70% reached a pooled state, and 5% percent dried completely during the sampling period. Samples collected from sites in the pooled stage included higher numbers of tolerant taxa and Coleoptera, fewer Ephemeroptera+Trichoptera (ET) taxa, and a much lower percent ET.  Up to two times the number of swimmer and predator genera were found in pooled streams. Changes in community composition during these stages present challenges for monitoring and justify the need to define an optimal index period for bioassessment of intermittent streams.