Story County Stream Monitoring, September 2026
Introduction
Prairie Rivers of Iowa and its partners are in the sixth year of a water monitoring project in Story County. This report includes data from 15 sites that we monitor monthly, with samples tested by a certified lab operated by the City of Ames for nitrate, total phosphorus, total suspended solids, and E. coli bacteria. It also includes data from three sites on the South Skunk River that are monitored weekly for nitrate, total phosphorus, and total suspended solids.
Our most recent results are from September 16. On the graphs below, these results are shown as red dots. The black square and line show the median and range observed at each site since 2020. The pale gray shape is a violin plot, which shows how the data are distributed.
Map
This interactive map shows the location of our sites. Click a point to see the latest data.
Sampling Conditions
Clouds for days, as far as the eye can see. Despite the damp weather, crops are browning fast, and some fields are already being harvested.
In the weeks leading up to our sampling event, discharge in the
South Skunk was relatively stable: a steady general decline, with a few
small spikes from rain on the 7th and 9th.
However, sampling coincided with a multi-stage rainfall event that
ultimately brought about 1.6 inches of rain to the area.
That rain on September 14–15 drove discharge up rapidly, from ~200 cfs to ~1,100 cfs at the time of sampling on 9-15. For this time of year, 1,100 cfs is in the 90th–95th percentile for discharge on the South Skunk, or “much above normal.” Once again, we sampled during a discharge spike and will likely see results driven by that timing.
Nitrogen
And we’re back in double digits! While most values are near average
compared with the full dataset, it’s important to remember the
seasonality of nitrate readings. When we narrow our scope of comparison
to just September, the story looks worse. 
We don’t have many September measurements for most sites (none for Worrell Creek and two to six for the rest), so this isn’t the most robust dataset. Still, you can clearly see that this sampling event captured unseasonably high nitrate, especially when you look at the larger data set from the South Skunk. As we noted last issue, nitrate levels typically bottom out in September. So what’s happening here?
The first answer is the rain. Typical rainfall in the fall is less than spring and summer. And as we noted, the spike in discharge was well above average for this time of year. It was by no means an anomalous rainfall, but it was enough to push nitrate into surface waters.
According to ISU Extension’s Forecast and Assessment of Cropping sysTemS (FACTS) data, the soil nitrogen mineralization rate (the conversion of organic nitrogen into plant-available forms like nitrate) in central Iowa was over 1.0 lb N/acre/day during this period. Brown crops don’t take up nitrogen, so any nitrate released accumulates in the soil, creating an unstable, leaky reservoir. Cue the rains, sample right at the start of the pulse in the hydrograph, and you capture the release of that concentrated nitrogen. It’s possible that the elevated levels here observed were short lived, but it’s impossible to know without more intensive monitoring.
As with our early-spring samples, these data point to a major
systemic issue with modern row-crop agriculture. Whether it comes from
fertilizer or mineralization, soil nitrate is especially vulnerable to
leaching when nothing is growing. To meaningfully reduce fall nitrate
losses, cover crops have to be planted and actively taking up nitrogen
well before harvest. Even now, the cover crops I have seen are far too
small to make a real dent in free nitrate in the soil. Low precipitation
in the fall usually keeps nitrate losses in check, but events like this
demonstrate how vulnerable our system is.
Sediment
Total suspended solids (TSS) is a measure of water clarity, determined by filtering a water sample and weighing the solid material left behind. That material is usually sediment (mud), but it can also include algae and other organic solids. TSS typically increases after rainfall because of erosion.
TSS was generally high, - as to be expected - reflecting the rain immediately preceding the sampling event.
Phosphorus
Phosphorus is an essential plant nutrient that contributes to algae blooms when it reaches the water. It is usually the limiting factor for algae growth in lakes and reservoirs. The laboratory test for total phosphorus has a lower detection limit of 0.1 mg/L.
Phosphorus was higher than average at many sites, likely related to the high TSS from recent rains. This month, I ran an additional correlation analysis across all sites and years to see how much of the variation in phosphorus levels can really be explained by sediment alone.
As the plot shows, TSS and phosphorus are correlated at most
sites. R², a measure of how closely two variables are related, ranges
from 0.03 at the low end to 0.54 at the high end; higher numbers
indicate a tighter relationship.
Interestingly, a few sites (the South Skunk River at 280th Street and 580th Avenue, and West Indian Creek at 280th Street) showed the reverse relationship, with higher TSS corresponding to lower phosphorus, although these relationships were weaker (R² of 0.07–0.13). Either way, it is clear that TSS alone can’t explain the phosphorus in the water column.
Bacteria
E. coli bacteria are an indicator of fecal contamination from human waste, livestock, pets, or wildlife, which can make people sick if they accidentally swallow water while recreating. Single samples are evaluated against a threshold of 235 colonies per 100 mL in waters designated for primary contact recreation, and 2,880 colonies per 100 mL in waters designated for secondary contact recreation. These thresholds are shown as yellow and red lines on the graph. The standards apply from March 15 to November 15, when recreation is possible; this is also when most wastewater treatment plants run their disinfection equipment.
For the second month in a row, E. coli numbers were very high, with all but five sites exceeding the secondary contact recreation standard. Every stream in our survey is designated for Class A1 (primary contact) recreation, so based on our data, every one of them would need to be listed as impaired.
If you’re interested in a deeper dive into E. coli and the species contributing most to the problem, be sure to check out the September issue of the PRI newsletter for an in-depth look.
Conclusion
Late-season rains over senescent crops led to a surge in nitrate, TSS can’t explain everything about phosphorus, and E. coli numbers remain astonishingly high.
Casey Greufe, Prairie Rivers of Iowa
September 24,
2026