Bioassessment Monitoring

 The Bioassessment Program is comprised of the three major components of water quality: 

  1. Biological – fish and macroinvertebrates, the bugs that live all or part of their lives in the water 
  2. Chemical – water and sediment samples 
  3. Physical – the structure of the segment of stream and the riparian area along it that represents habitat.   

This program is meant to collect long-term data so that we can see trends over time and document incremental improvements as projects or other management changes are implemented. We typically sample watersheds every three to five years. 

Identifying Monitoring Sites

The first step in designing a Bioassessment Program for a particular watershed is to identify sites that represent different stream sizes, land uses and specific conditions.  We use a geometric design to create a base layer of sites based on drainage area.  For example, if a watershed has a drainage area of 100 square miles, we would cut that in half and put a site where the drainage area is 50 square miles, then cut it in half again and put a site where ever the drainage area is 25 square miles etc. until we get down to a 2-5 square mile drainage area. This geometric design gives us an even distribution of sites based on drainage area and is a relatively simple mapping exercise.   

Now we need to get a little more personal with the watershed and add in targeted sites around things that potentially impact water quality. This could be upstream and downstream of a wastewater treatment plant, a major tributary or a dam. It could also be in a preserve that represents a high-quality area that was missed by the geometric design.  

Once we get the sites on a map, we need to make sure we can actually get to them, so we usually try to associate a site with a bridge to make water sampling easier. We also need to make sure we can get sampling equipment safely into and out of the stream and get permission from landowners to access the stream.  This part usually requires us to go and visit each site to determine how suitable it is for sampling.  All of this, plus all of the documentation, permits and contacting the landowners, needs to be done before collect our first sample. 

What We Sample

Now that we know where the sites will be, what and how do we sample?  


Chemistry is the bookends of our sampling season. We start sampling water chemistry as early as May through early September. We collect between two and eight samples at a site depending on how complex the site is. For a small tributary site with a drainage area of 2-7 square miles without any major discharges into it, we will collect a sample twice through the summer. For a larger site or upstream and downstream of a wastewater treatment plant we may sample as many as eight times through the summer.

We collect a suite of parameters including nutrients like phosphorus and nitrogen, dissolved oxygen, temperature and conductivity as well as metals and chlorophyll-a. These samples give us a snapshot of the water chemistry on a particular day. We also collect a surficial sediment sample in October to give us a picture of what has been deposited over the year. Many pollutants attach to sediment particles and are deposited is slower moving areas. In addition to many of the water chemistry parameters we also sample for pesticides, volatile organic compounds and PAHs in sediment. 

Fish, Macroinvertebrates, and Habitat

Fish and macroinvertebrate sampling is generally done from late June to mid-September during the low flows of the summer. Fish are collected using electro-shocking methods suited for the size of stream ranging from a boat mounted unit to a small generator in a raft to a back-pack unit.  The length of the sample site is based on the width of the stream, the wider the stream the longer the segment. Fish are mildly stunned with the electric current and scooped up in nets and held in tubs of river water until the whole sample is collected. All of the fish are identified, counted and weighed before being released back to the stream. 

The crew that collects the fish will also complete the Qualitative Habitat Evaluation Index field sheets. This index looks as eleven different components of habitat including substrate, flow, refugia (places for fish to hide or get out of high flows,) riffles, pools and riparian quality. Each component is scored 1-10 and then totaled to provide a relative habitat score. 

Macroinvertebrates are sampled by a second crew using a D-net to sample all available habitat within the sample site. Habitat areas would include riffles, undercut banks, overhanging vegetation or in-stream plant beds as well as picking up rocks to see who is hanging out on the bottoms. All of the macroinvertebrates collected are preserved in alcohol and taken back to the lab for identification.  

Continuous Dissolved Oxygen

In addition to the Bioassessment Monitoring Program that happens every three to five years there are a number of permanent or semi-permanent Continuous Dissolved Oxygen (DO) Sites. This program has been under way in the Lower DuPage from 2014 and started in 2021 for the Lower Des Plaines.

The Continuous DO program uses multi-parameter probes that are deployed in protective housing attached to bridges. The probes have sensors for dissolved oxygen, water temperature, pH and specific conductivity. Some probes also have turbidity and chlorophyll-a sensors. The probes are programed to collect data once an hour, 24-7, from spring through late fall. This continuous data is able to document the diurnal (24-hour) cycle of dissolved oxygen in the stream. This is important because oxygen levels can fluctuate from low levels in the pre-dawn hours to very high levels in the late afternoon. This cycle is driven by the amount of algae and aquatic plants growing in the stream as they use and expel oxygen through respiration and photosynthesis. Some fluctuation is normal (6-10 mg/l), but large fluctuations can be stressful to aquatic life, particularly when early morning values are below the state water quality standard of 5 mg/L of dissolved oxygen.  

Chloride/Conductivity Monitoring

The multi-parameter probes can also be used at some locations in the winter to track changes in specific conductivity. Specific conductivity can be a good proxy for the amount of chlorides in the water, particularly in the winter time when rock salt is applied to roads and parking lots. As snow melts the salt is carried to the river via storm sewers and can cause problems for aquatic life. Continuous conductivity data paired with weather data correlates very well showing the increase in chloride levels during and after a storm.