The Bioassessment program currently classifies sampling sites in three categories- Wadeable, Headwater, and Large River.

1. Wadeable - As the name implies, these streams are easily wadeable by the sampling crew. They range from ankle-deep and a few feet across to larger rivers that may be chest deep. Most of these streams are sampled using one or more electroshocker backpacks, while the deeper streams require a 'barge' shocker- which is a small, floating craft with a generator and the shocking equipment built into it. Streams that are shocked using the barge will usually be used in conjuction with backpack shockers to reach the shallower fringe areas.
2. Headwater - A pilot program was begun in 2007 to sample the headwater areas of streams. These areas are typically shallow and narrow, with a very small watershed area. The fish and benthic macroinvertebrate assemblages in these areas are usually quite different from those found further downstream. The Iowa Department of Natural Resources is currently in the process of developing an Index of Biotic Integrity (IBI) calibrated to these headwater streams.
3. Large River -(Formerly known as Non-Wadeable) - At the downstream-most ends of the larger rivers, these sites are typically only sampled using a boat outfitted with electroshocking equipment. Because of the nature of this equipment and the larger, deeper water, sampling is skewed towards larger fish species. Benthic macroinvertebrate sampling is also very difficult, as most areas are inaccessible to the sampling crew. A fish IBI is in development for these sites.