How We Conduct Annual Bioassessments

sediment sampling

As the year draws to an end we also draw to the end of our annual bioassessment. The bioassessments are intensive watershed wide surveys of aquatic life, physical habitat, and water and sediment chemistry. Our watersheds that we study represent hundreds of square miles in drainage area and have a complex mix of overlapping stressors from various sources in a highly urbanized landscape. Conducting a bioassessment takes several months to complete for each watershed.


The Conservation Foundation and the watershed groups it staffs conduct bioassessments in six different watersheds. The East Branch DuPage River, West Branch DuPage River, Lower DuPage River, Salt Creek, and the Lower Des Plaines River and its tributaries. This represents over 1,000 square miles of watershed, which is much more area than can be surveyed in a single summer by our humble field team. Therefore, all the watersheds are surveyed on a rotational schedule that results in a complete survey of all watersheds every couple of years. Once we cycle through all the watersheds, the process repeats and we continue to build our database of long-term information. It’s important to continuously run the bioassessments as it allows us to identify long term trends in the data, and determine if we are having any impact as we complete restoration projects and pursue our goals.


Planning starts in the spring, when we visit our identified sites. Site visits are important because placement of sites is typically done on a map and is based on locations that are statistically comparable to each other. Additional sites are added around points of interest such as treatment plant outfalls, dams, or anything else that will have a significant effect on the river. As such, more practical considerations such as property access, determining if the site is representative of the river, and making sure sites haven’t changed between bioassessments is important and must be done in person. Each watershed has around 30 – 40 sites depending on the size, while the Lower Des Plaines has well over 100 due to how large it is (the Lower Des Plaines is on its own rotation where we complete that watershed once every few years).


Once the sites are identified we begin our chemistry sampling. Water samples are collected multiple times from every one of our sites, from May through August. We are testing those samples for things like chloride, dissolved oxygen (DO), pH and dissolved solids, as well as nutrients like nitrogen and phosphorus. We also test for numerous metals such as calcium, iron, lead, mercury, or zinc, and other organic compounds like pesticides and volatile organics. Many other parameters are included as well to get a thorough picture of instream chemistry.


During this time, we also have our fish and macroinvertebrate (Aquatic Insects) crews out sampling. The fish crew uses electrofishing equipment, either in the form of a raft or backpacks, to send mild electrical pulses through the water. Fish in the vicinity are temporarily stunned and float to the surface. From there, the fish crew scoops them up and places them in large buckets where they resuscitate, and then the fish are identified, counted, and weighed. This gives us a very good idea of how many fish species and amount of fish are present. Afterward, the fish are released into the river. As violent as that may seem, it is very uncommon for the fish to suffer fatalities from this process. Even in areas where people swear they’ve never seen even a single fish, they are surprised at how many are lurking out of sight and caught with this technique.


While less intense than electrofishing, the macroinvertebrate crew also plays a crucial role. They use dip nets to scour small patches of the river bed in carefully determined areas to find communities of tiny aquatic insects. These are the larval stages of things like dragon flies and damsel flies, and include some really unique creatures. They typically like to live in rocky, gravel bottom stream beds. Rivers bottoms that are covered in mud tend to have more things like flatworms and black fly larva. They collect the macroinvertebrates, and then spend time identifying them under microscopes. Identification to species is extremely difficult and requires a trained eye.


Fish and macroinvertebrate sampling are important because some species are very sensitive to pollution and some are very tolerant. So, if our sampling turns up a lot of pollution-sensitive species at a site, we know there is very little pollution there. And if we have only pollution tolerant species at a site, then there is high pollution and we likely need to investigate a restoration project for that area.


When July starts, we begin our Expanded DO portion of the bioassessment. From our large list of sites, a subset of sites is identified for more intensive monitoring. We place a continuous data sonde at each site to record several parameters every 15 minutes for a minimum of 7 days. During that deployment, our field team visits the site and records data on physical habitat, hydrology/flow data, and collects benthic algae samples and a water sample with additional parameters. The expanded DO sampling must be completed by the end of august, as our data requires low flow conditions in the rivers. It makes for a whirlwind of a summer with little room for delays.


Once September comes, most sampling must be complete and the bioassessment takes a pause until October, when we start sediment sampling. Sediment sampling is intended to capture the sediment deposits that accumulate within the river over the past year. Actual sample collection is more of an art than a science as it is very difficult to skim only the last 12 months’ worth of sediment deposits from the bottom of a very silty stream. But after sediment is collected it is run through a fine mesh sieve and allowed to decant before being bottled and sent to a lab. Sediment samples are tested for many of the metals and organics that water samples are tested for, but many compounds attach differently to sediments versus water and in different forms, so both are necessary. While sediment sampling is very dirty work as I am essentially sifting mud, it is my favorite as I get to set up at a site and hang out in the river all day surrounded by autumn trees with very few other disturbances. Sediment sampling must be completed by the end of the year, and the sooner the better. It gets very difficult to break through the ice to collect sediment come December.


With the completion of sediment sampling and the bioassessment, our attention turns to data analysis for the winter. Results roll in from the lab, trends are analyzed, and we produce a comprehensive report about the condition of the watershed. For anyone looking to get an in-depth review of their watershed, visit the watershed group’s website ( where all the reports are posted when completed.



The fish crew electrofishing with a raft on the East Branch of the DuPage River.



The field crew conducting Expanded DO sampling on what turned out to be the hottest day of the year.


sediment sampling

Sitting in the river and collecting sediment samples.


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