How Big is the Elephant in the Room?

by Dan Haug | May 15, 2024

Iowa has a lot of hogs, poultry and cattle raised in concentrated animal feeding operations (CAFOs). They produce a lot of manure. However, CAFOs are not evenly distributed across the state, and it’s rarely practical to haul the manure long distances. Do rivers with more CAFOs in the watershed have worse water quality? I was curious and recently completed a big data analysis project to find out. I’ve omitted some of the technical details in the interests of making this article easier to read, but hope to eventually submit this research to a scientific journal for peer review. Get ready for a nuanced, data-driven look at the elephant in the room!

Livestock Density by Watershed

The water quality data for this study comes from 60 sites in Iowa DNR’s ambient stream monitoring network. (Two sites were later dropped because of incomplete data). For each monitoring site, I delineated a watershed (the land draining to that point) and overlaid databases of animal feeding operations. CAFO density in these watersheds varies greatly: from 12 animal units per square mile in Cedar Creek near Bussey, to 883 animal units per square mile in the Floyd River near Sioux City.

Animal units are a way of standardizing herd size across ages and species. For regulatory purposes, one 1000 pound steer is equivalent to 10 pigs under 55 pounds, 2.5 pigs over 55 pounds, 55 turkeys, or 82 layer hens. Feedlots with at least 300 animal units are tracked in Iowa’s database. Feedlots with 500 animal units require a manure management plan, and feedlots with 1000 animal units require a construction permit. The Iowa Environmental Council continues to follow and raise concerns about these rules.

Initial Findings and Complications

In the article that inspired this project, “The Fair, the Marginal, and the Ugly”, Chris Jones used this same dataset to rank water quality in Iowa’s rivers and noted that the river with the worst water quality has the most CAFOs. The Floyd River had the highest nitrogen and total phosphorus, the third highest turbidity, and the sixth worst E. coli. Sticking with the same time period (2016-2020) and similar metrics, I plotted water quality against livestock density for 58 sites to see if the Floyd River is part of a larger pattern. For nitrate, yes; for total phosphorus, maybe; for turbidity and E. coli, no. The relationship with turbidity is weakly negative; rivers with muddier water actually tend to have fewer CAFOs in the watershed.

The best explanation for this is that there is a third factor influencing both water quality and CAFO density: terrain. CAFOs are most common in flatter parts of the state where construction permits are more likely to be approved and there is plenty of cropland nearby to spread the manure. The notable exception to the pattern is Bloody Run, a trout stream in northeastern Iowa. In 2021, the Iowa DNR approved the construction of a 11,600 head cattle feedlot in this watershed, despite the steep terrain and abundant sinkholes. Given the timing, I am excluding this site from analysis and hope we do not have to find out what happens to water quality when this much manure is added to an environmentally sensitive area.

Slope and cropland are also correlated with livestock density.

Primary drivers of water quality

To better understand the interactions of multiple variables without a lot of statistics, I like to color-code one of them (in this case, CAFO density) and then focus on a narrow range (in this case, watersheds with less than 160 animal units/square mile). You’ll see this technique several times in this article. This shows how slope and cropland in the watershed influence water quality, independent of CAFOs.

Slope: As you’d expect, turbidity in rivers is strongly correlated with the average slope of land in the watershed. Steep hills are more susceptible to runoff and erosion. Phosphorus and E. coli are also attached to sediment and carried by runoff, so are moderately correlated with turbidity, and weakly correlated with slope.

Cropland: Nitrate in rivers is strongly correlated with corn and soybean acres in the watershed. Long-term nitrate trends can also be explained by changes in cropping patterns (a replacement of hay and small grains with corn and soybeans). I’ve heard corn and soybeans described as a leaky system, and want to echo that. Whether the nitrogen comes from manure, ammonia, or soil organic matter, if you don’t have something green and growing in the early spring, you’re going to lose a lot of it.

Graph of turbidity vs slope for watersheds with few CAFOs

Nitrate vs cropland in watershed, for watersheds with few CAFOs

Manure and Bacteria in the Water

E. coli is a bacteria found in the guts of birds and mammals, an easy-to-measure proxy for poop in the water and the pathogens that might come with it. For many environmentalists, the reason for Iowa’s long list of impaired waters seems frustratingly obvious. Hogs, poultry, and cattle outnumber humans, dogs, geese, raccoons, and deer, so they must be the main source of E. coli. Here’s an example of that kind of thinking from a report by the Environmental Integrity Project.

“Iowa is America’s hog capital – and also one of the most unhealthy areas in America to swim in rivers and streams. That’s in part because of the vast amounts of hog waste and farm runoff polluting the state’s waterways.”

The same logic showed up in the watershed management plan for Ioway Creek (and some others like it), which assessed likely bacteria sources based on the population of various kinds of animals and the amount of manure they excrete per day. While the consultants were careful not to say that hog confinements in Hamilton County were the main reason for chronically high E. coli in the creek, I sure got that impression from reading the maps and tables.

Looking at livestock populations turns out to be an unreliable way to guess which rivers will have bacterial impairments. Statewide, there is no correlation between E. coli in the river and livestock density in the watershed. The three worst rivers for E. coli in this dataset (the Soldier River near Pisgah, Maquoketa River near Maquoketa, and W. Nodaway River near Shambaugh) have less than 320 animal units per square mile, on the low side for Iowa.

More sophisticated models take into account the fraction of manure that reaches streams, how long it takes to get there, and how much of the bacteria dies off in the meantime. Unsewered communities, geese on the beach, raccoons in the storm sewer, and cows wading in the creek produce much less manure than animals in CAFOs, but a larger fraction of the manure is delivered directly to the water when it’s still fresh. That’s not to say that manure from CAFOs have no influence on E. coli in rivers. Once rivers with slopes steeper than 4% were excluded, the remaining sites had a moderate correlation between E. coli and livestock density.

E. coli vs livestock density for sites with less than 4% slope

Manure Nutrients in the Water

If manure is applied to fields that are not too steep and set back from streams, during appropriate weather conditions, and especially if the manure is knifed into the soil, very little of the solids, E. coli bacteria and pathogens in the manure should reach streams. The same is not true of the nutrients in the manure. Nutrients cycle between different forms, and the more readily dissolved forms (nitrate and orthophosphate) can easily leak out of the root zone during periods when crops aren’t growing, and make their way to streams.

Watersheds with a high density of CAFOs tend to have much higher nitrate concentrations, but most of that is because those watersheds also have a large proportion of the land in row crops. However, focusing on sites with at least 80% of the watershed in row crop production, there is still a positive correlation between livestock density and both nitrate and total phosphorus.

In the science assessment for the Iowa Nutrient Reduction Strategy, manure was not treated as a challenge for nutrient reduction, it was treated as a best management practice. It makes a certain amount of sense: manure is a slow-release fertilizer that adds organic matter to the soil. Compared to plots fertilized with commercial fertilizer, plots fertilized with swine manure had 4% less nitrate loss by 46% less phosphorus loss, mainly due to soil improvements that reduced the amount of runoff. However, those agronomic trials must have used a different set of application rates than usually occurs in practice. If you look at both commercial fertilizer sales and manure availability, counties with many CAFOs apply nitrogen and phosphorus at higher rates, with consequences for water quality. Here’s one study from Minnesota and another from Iowa that document this.

Closing thoughts

Prairie Rivers of Iowa has worked with some large swine and cattle producers who were early adopters of cover crops and who are very careful about how they manage manure. We salute their efforts to improve soil health and protect water quality. A study like this can only address the impacts of the industry as a whole.

Swine manure leaked into a creek in Greene County in summer of 2023.

This project was funded in part by a research grant from the Raccoon River Watershed Association, which has been monitoring water quality in Greene County. Last summer, the group watched with alarm as hog manure leaking from an earthen storage basin turned the water in a creek brown and caused the dissolved oxygen in the water to drop to zero. These kinds of incidents happen way too often, but usually affect a small stretch of stream for a short period of time, so don’t show up in monthly water quality datasets.

The correlations between water quality and livestock density disappeared entirely when I looked at two drought years (2021-2022). During dry periods, runoff and tile drainage from farmland is minimal, but effluent from sewage treatment plants and industry (including meatpacking plants) can have a bigger influence on water quality. Manure from CAFOs definitely impacts water quality in Iowa, but if we’re too quick to blame them in every situation, we may miss what’s really going on.

South Skunk River Cleanup – Spring 2024

by Dan Haug | Apr 24, 2024

16 people participated in the cleanup (2 not pictured, photo credit: Jake Moore)

On April 20, volunteers cleaned up trash along a 3.5 mile stretch of the South Skunk River in Ames, from River Valley Park to S. 16th St. Several people also ventured up Ioway Creek, and those who stayed on shore had plenty to do. The fast current meant we arrived at the destination earlier than expected, where we set to work clearing out an abandoned campsite. Judging by some of the items we found, families with children had stayed there, so please support organizations that work on affordable housing and provide emergency assistance. In between stops at sandbars to retrieve trash, there was ample opportunity to enjoy the river. The fast current made for a fun ride through some mini-rapids (nobody tipped!), and we saw kingfishers, great blue heron, and a bald eagle.

Volunteers launched canoes at N. River Valley Park in Ames (credit: Liz Calhoun)

Chilly weather (high of 48 degrees) may have dampened some of the initial enthusiasm for our spring 2024 creek cleanup event. We went from having not enough canoes for everyone who registered, to several extra canoes. With a smaller flotilla than last spring, we can’t claim a record breaking haul, but we did remove more more trash per person! In addition to the usual cans, bottles, plastic and styrofoam, finds included four tires, seven empty propane tanks, a shopping cart and a microwave.

April 2023: 3,020 pounds/40 people = 76 pounds/person
April 2024: 2,100 pounds/16 people = 131 pounds/person

Tony Geerts likely exceeded that average figure, arriving at the take out point with a big tractor tire. It would have made a great picture, but as I was rushing up to capture the moment, my phone slipped out of my hands and into the river! Fortunately, other people took photos and have shared them with me.

Volunteers with 2500 trash removed from South Skunk River

Assembling the tools, canoes, food, and people was a collaborative effort involving Prairie Rivers of Iowa, the City of Ames, Story County Conservation, the Skunk River Paddlers, and the Outdoor Alliance of Story County. Thank you to all who volunteered, organized, and supported the event.

Water quality results for 2023 in Story County

by Dan Haug | Apr 15, 2024

Our 2023 Annual Report is now available with results of both volunteer and lab testing of water quality in lakes and streams in Story County. The 56-page report can be navigating by clicking on headings in the table of contents or by using the “Bookmarks” feature in your PDF reader. Below are some of the key findings.

Amelia Whitener leads a water monitoring demonstration at a trash cleanup event.

The volunteer program continues to grow and improve in consistency.

49 volunteers entered 969 data sheets into the Clean Water Hub this season.
Many volunteers are monitoring their assigned site biweekly, with 20 sites sampled at least 20 times.

Mayfly larvae (nymph) under magnifying glass

This was a challenging year for fish and aquatic insects.

In addition to many creeks drying up, volunteers observed dissolved oxygen drop to low levels at 53% of stream sites.
Biological surveys showed mixed results, with some streams scoring poorly but sensitive insects like mayflies present in others.

Cows with access to creeks are one possible source of E. coli bacteria

E. coli bacteria levels in streams remained high.

All thirteen streams with enough data to evaluate this season exceeded the primary contact recreation standard. Three streams exceeded the secondary contact recreation standard: (West Indian Creek, College Creek, and Ballard Creek.
However, over the last four years, most sites on the South Skunk River meet the standard when there is enough water to float a canoe.

UV disinfection system at Ames Water Pollution Control Facility

Wastewater treatment plants are not yet capable of removing some of the pollutants we monitor, and can have a large influence during drought when effluent is less diluted.

Effluent from the old sewage treatment plant in Nevada was found to be a major source of E. coli bacteria. The new plant, currently under construction, includes a disinfection system that should address the problem.
Stream sites downstream of sewage treatment plants tend to have elevated chloride and phosphate.

The encouraging trends we noted in the 2022 report held up with another year of data. Water quality trends are often driven by weather, but we pulled out subsets based on streamflow to remove some of this influence.

E. coli in the South Skunk River below the Ames Water Pollution Control Facility has improved relative to the pre-2014 baseline period, especially during dry conditions when wastewater has the greatest influence.
Nitrate in the South Skunk River below the confluence with Ioway Creek improved relative to the pre-2014 baseline period, even after excluding dry periods. This pattern is consistent with improvement from conservation practices.

Paddling While Impaired

by Dan Haug | Mar 16, 2024

For safety’s sake, I wish people would not mix boats and alcohol, but I’m writing about the other type of impairment that can get in way of having a fun and safe experience on Iowa’s lakes and rivers: water quality. Every two years, the Iowa Department of Natural Resources takes stock of which lakes and rivers have water quality good enough to fully support recreation, fishing, drinking water supply, and other beneficial uses. Those that don’t go on the Impaired Waters List. The draft 2024 Impaired Waters List has been published and you can make public comment through April 12.

Understanding the numbers

Most of the op-eds and news stories about the impaired waters list focus on the numbers. There are 572 rivers and streams, 137 lakes, and 12 wetlands on the impaired list. If you had forgotten that Iowa has water quality problems, here’s your biennial reminder!

This year, there are fewer impaired waters than in the 2022 cycle. Much will be made of that, and will be much ado about nothing. The Impaired Waters List is not very useful for evaluating water quality trends, because the number of waters assessed and the methodology used to assess them is always changing. It’s also worth noting that the assessment period (2020-2022) included long stretches of drought, which means less runoff, so it’s possible that some of the 97 waters removed from the list will go back on the impaired list when we get some wetter weather.

Missing data

Not too long ago, the biggest category in the integrated report was waters not assessed. This year, it has dropped to 49% of rivers, 44% of lakes, and 21% of wetlands. We can claim a little bit of credit for this. Eight stream segments formerly in the not assessed category were tested for E. coli as part of the Story County water monitoring program and are now in a category called Waters in Need of Further Investigation (WINOFI). There’s a state law that prevents IDNR from using third-party data for regulatory decisions, but I still appreciate that they reached out and included our data in the report!

An example of Waters in Need of Further Investigation (WINOFI)

Seasonal E. coli averages for West Indian Creek, from our local monitoring program.

Finding clean waters

I’m most interested in which waters are impaired and why. For rivers, the leading cause of impairment is E. coli bacteria, an indicator of fecal contamination and a proxy for other pathogens that could potentially make people sick if they swallow some water while recreating.

I am sometimes asked where to go in Iowa to find clean water for paddling, swimming, floating in an inner tube, or just letting the kids splash and catch crayfish in the creek. A map or list of impaired waters is not very helpful for this, because the waters that aren’t included might be clean, or they might not have been assessed. So I made an interactive map, color-coded to show which lakes and rivers met or exceeded the primary and secondary contact recreation standards, in the last four recreational seasons. Hopefully this a just a prototype for something even better and more comprehensive.

Improving Impaired Waters

We don’t want to just avoid the impaired waters, we want to know how to clean them up. The Impaired Waters List is also a waiting list for a water quality improvement plan, or Total Maximum Daily Load (TMDL). IDNR has studied swimming beaches at several lakes (including Hickory Grove Lake in Story County), and found that E. coli is highest in the wet sand at the beach, and lower in the lake and tributaries. For these lakes, that suggests that the biggest sources of contamination are located at the beach, things like geese and diaper malfunctions. For rivers impaired by E. coli, we don’t know the cause. Many rivers have been waiting decades for a TMDL in a low priority tier, and a TMDL that was written in 2017 for the Iowa River seemed incomplete.

However, after attending the Raccoon River Watershed Association’s annual conference on March 9, I no longer feel like Iowa has given up on recreational water quality in rivers. Robin Fortney shared reminiscences of many river trips. Jon Wenck (IDNR) and Pat Boddy (ICON) talked about Iowa’s growing network of water trails. It’s clear there are people who care about our rivers and see how they can benefit quality of life and economic development. Claire Hruby (Drake University) shared some early results from microbial source tracking and microbial risk assessment research in Polk County. With these approaches, can find out which pathogens are present in the water (not as many as we feared) and whether waste is coming from livestock, wildlife, or humans or a combination!

My contribution to the conference was a nuanced look at exactly how CAFOs (big feedlots) impact water quality. I hope to share a video of the presentation and a report in our April newsletter. There are far too many spills and leaking manure storage structures, and manure management plans don’t prevent over-application of nitrogen and phosphorus. However, the claim that waste from factory farms is responsible for most of Iowa’s impaired waters is just not supported by the data. Here is one figure from my presentation. Notice that Iowa has many rivers with extremely high E. coli levels but fairly low livestock densities in the watershed. To understand E. coli contamination, you have to consider not just the amount of feces produced, but how it likely it is that feces will reach the water before the bacteria die off.

Graph of E. coli vs livestock density in 58 Iowa watersheds

The Fine Print

If you explore the Impaired Waters List and the rest of the assessment database, you will likely run across some things that don’t make sense. I share your frustration! This pair of short videos from our “Clean Water Act: 50 Years, 50 Facts” series contrasts how Section 305(b) and 303(d) of the Clean Water Act should work in theory, and how it can go wrong in practice. However, I continue to see improvements in the assessment database (ADBNet) and water quality database (AQuIA) and want to express my appreciation to IDNR for the data they collect and their efforts to be make it available to the public.

Green Stuff in the Skunk River

by Dan Haug | Mar 14, 2024

On Tuesday, March 12, residents on the north edge of Ames noticed that the South Skunk River was cloudy and had turned an unusual shade of bluish green. By the time I looked at it on the afternoon of March 13, the color had faded and the water was less cloudy, but it still had a soupy, streaked appearance that I’ve seen before in lakes following a toxic algae bloom. I’m gonna go out on a limb here and say it’s blue-green algae (cyanobacteria).

Cyanobacteria bloom in the South Skunk River

Cyanobacteria bloom, showing paint-like streaks.

“Algae” is a word that gets lazily applied to any living thing that does photosynthesis but that isn’t a plant: from tiny glittering diatoms in a drop of pond water to giant kelp in the oceans. The other kind that I noticed in the South Skunk River this week is filamentous green algae, which forms slimy hair-like strands on rocks and globs on the water’s surface. Color is the least of the differences.

Cyanobacteria are tiny and simple. There’s strong evidence that the chloroplasts in the cells of plants and green algae are the captured descendants of cyanobacteria. This amazing phenonemon is called endosymbiosis, and it’s happened multiple times in the history of life on earth. If you’ve never heard of it, I’d recommend this YouTube video, which explains the concept with cartoons.

The practical reason to know if the green stuff in the water is cyanobacteria is because they can produce toxins. I wasn’t able to get a sample tested for microcystin (and chances are, this algae bloom will have dispersed by the time you read this), but I would recommend keeping your dog out of water that looks like paint or pea soup, to be on the safe side.

Green algae in the South Skunk River (Rick Dietz)

A simple guide for green stuff in the water.

Why is the water so green, so early? Algae growth is limited by the availability of light, heat, and fertilizer–phosphorus in freshwater, and to a lesser extent nitrogen. We’re getting unseasonably warm weather before there’s any leaves on the trees to shade the water. As for the fertilizer, I’m not sure where it came from, or when. Rick Dietz and I tested nitrate and phosphate with field kits on Wednesday and measured 0 mg/L. Nitrate and phosphorus levels were also fairly low at this site when we collect grab samples in February. Maybe something was washed into the river earlier in the week, but it has since been used up by the algae or has washed downstream. I’ll amend this article if I find out something conclusive.

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