Transition briefing · Public health and environment

Continuous microbial water quality monitoring for Colorado

Prepared for the Weiser transition, November 2026 · Evan Thomas, PhD, PE, MPH, University of Colorado Boulder and Virridy

Summary

Colorado decides whether rivers, swim beaches and emergency water supplies are safe from fecal contamination with grab samples that take a day to culture and are collected weekly to monthly. A continuous fluorescence method now validated against the EPA's own acceptance test can report the same risk every few minutes. Several Colorado institutions are already using it: CDPHE's Water Quality Control Division is reviewing a plan to adopt it for Boulder Creek, Denver Water has it on its South Platte supply, and the Colorado National Guard is discussing a pilot for emergency drinking water. The same CU Boulder team supported CDPHE in the green infrastructure study required by Senate Bill 24-037, whose final report reaches the new administration in early 2027.

The gap in Colorado today

E. coli is the state's indicator of fecal contamination in recreational water. For primary contact streams Colorado's standard is 126 per 100 mL, expressed as a two-month geometric mean², and the 303(d) listing method generally needs five or more samples in a two-month period to place a segment on the list or take it off. A segment sampled less often than that often cannot be decided either way, which is what the 60 insufficient information units reflect.

At state park swim beaches, Colorado Parks and Wildlife closes a beach when a sample exceeds 235 per 100 mL, and samples are taken every two weeks³. A closure follows a lab result that describes water from the day before, and the beach stays closed until a later sample comes back clean.

In emergencies the same lag applies to drinking water. When the September 2013 floods overran the sewer system in Lyons, officials said the drinking water was compromised while the Colorado National Guard was evacuating residents⁴. Confirming that a supply is safe again depends on coliform cultures run in a lab, at the moment roads and labs are hardest to reach.

Where Colorado measures today

Every monitoring location in Colorado with fecal indicator records in the public Water Quality Portal, as compiled by Open Water Quality¹¹, drawn over the WaterNet stream network¹². WaterNet maps waterways from 20 m satellite imagery with deep learning and includes small streams missing from older maps. Of 1,884 sites, 1,214 have ever been sampled for E. coli; the median site has 4 E. coli samples in its whole record, 808 have fewer than 10, and 288 have any E. coli data since 2020.

Geometric means are over each site's full record, which for most sites is a handful of samples spread across years, so the colors show where E. coli has been found high, not current conditions. Click a site for its record.

The method

Tryptophan-like fluorescence (TLF) is light emitted by organic matter associated with fecal contamination. A submerged optical sensor measures it continuously, and a calibration against paired culture samples converts the reading to an E. coli estimate. The method is described in a manuscript under review at ES&T Water⁶.

EPA's technical support materials for site-specific alternative recreational criteria let a state adopt a different indicator or method if it agrees with the reference method at an index of agreement of 0.7 or higher on at least 30 paired environmental samples⁷. The adopted criterion keeps the existing numeric value, so the 126 standard stays in place and only the measurement changes.

The EPA threshold is 0.70. At the in-stream alarm level the sensors identified 83% of exceedances, with 68% specificity⁶. These figures come from Boulder Creek and from laboratory chamber tests; each new site is calibrated against its own paired grab samples, which is also how the EPA process works.

The method does not replace culture testing. Monthly paired samples continue at every site to check the calibration, and a positive sensor signal tells crews where and when to sample.

Work already under way

CDPHE and the City of Boulder: the regulatory pathway

Boulder Creek Segment 2b was Colorado's first E. coli TMDL, approved by EPA in September 2011⁸, and the reach remains impaired. The City of Boulder and CU Boulder have a joint project plan to ask the Water Quality Control Commission to adopt TLF as a site-specific alternative indicator for the segment, keeping the 126 standard year-round. All 2026 paired analyses were run in a CU Boulder laboratory, the single validating laboratory the EPA guidance allows⁷.

The plan follows the Commission's Policy 25-1 for external proposals⁹. The issue goes to the November 2027 issues identification hearing, with a target of the June 2029 South Platte basin rulemaking (Regulation 38). We found no state that has yet adopted an alternative indicator under the 2014 EPA guidance, so CDPHE would be setting the precedent, and a Division staff lead with time assigned to it is the main thing the proposal needs from the state.

Denver Water and Denver's public health department: source water and urban streams

Denver Water installed continuous sensors at three locations on its South Platte supply in October 2026, pairing a TLF unit with a dissolved organic matter unit at each. The City and County of Denver's Department of Public Health and Environment ran sensors on the South Platte and Bear Creek during 2026, paired with its own Colilert samples. Together these give the Front Range a working record of continuous microbial data on a supply that serves 1.5 million people⁵, and of recreational reaches in the urban core.

Colorado National Guard: emergency drinking water

The Guard is the state's response force for floods and wildfires, the events most likely to compromise drinking water. Mike Bunting of CU Boulder's Center for National Security Initiatives has recommended a funded pilot through the Guard's United States Property and Fiscal Officer, whose contracting office buys on the Guard's behalf. A small commercial purchase can proceed once the Guard names a unit that owns the requirement and identifies funds. The same sensors are in testing with the Air Force Research Laboratory, on loan to the Army's 25th Infantry Division, and the subject of a cooperative research agreement with the Army's Soldier Center that is in final signature, so a Colorado pilot would draw on federal military evaluation already under way.

Senate Bill 24-037: green infrastructure pilots

Senate Bill 24-037 directs the University of Colorado and Colorado State University, with CDPHE, to study alternative compliance programs that use green infrastructure and to establish up to three pilots¹³. The CU Boulder team held weekly check-ins with CDPHE through 2025 and in December 2024 completed a feasibility study ranking candidate pilots; Longmont, a Steamboat Springs water quality trading program and Plum Creek scored highest. CDPHE approved three regional pilots on a three-year timeline, a draft report went to CDPHE in October 2025, and the final report is due in early 2027. The City of Longmont has applied to host a demonstration project. An analysis of how water quality trading experience applies to the bill is published in JAWRA¹⁴.

In the team's survey of 167 practitioners and 27 interviews, regulatory constraints were the barrier to nature-based water quality solutions named most consistently, and respondents asked for continuous monitoring to set baselines and measure the effect of restoration¹⁵. The pilots are where that monitoring would first show results: a green infrastructure credit in an alternative compliance program depends on demonstrating the water quality change it buys.

A statewide program in three tiers

All three tiers should publish to one state data platform maintained by CDPHE, open to the public, so the same reading serves a permit holder, a park manager and an emergency manager. Culture testing continues at a reduced, fixed schedule at every site as the calibration and audit check.

Equipment cost is small relative to sampling labor. At Virridy's published price of $2,400 per sensor per year, a 50-site first phase costs $120,000 a year for sensors and data. The paired laboratory samples are an added cost that depends on how each agency runs them. Procurement should be competitive and specify the method and its EPA acceptance test, so that any sensor meeting them can bid.

First 100 days

Disclosure

Sources

1. US EPA, ATTAINS assessment data, Colorado 2024 reporting cycle (EPA final action), queried 10 November 2026. 78 assessment units list E. coli as a cause of impairment; 60 list E. coli as insufficient information. epa.gov/waterdata/attains
2. Colorado Water Quality Control Commission, Regulation 31, 5 CCR 1002-31, Table I, footnote on E. coli two-month geometric mean; and the Commission's 303(d) Listing Methodology, 2026 cycle. cdphe.colorado.gov
3. Denver7, "Swim areas at Chatfield, Cherry Creek State Park closed due to elevated E. coli levels." denver7.com
4. CBS Colorado, "National Guard airlifts thousands from flooded Lyons," 13 September 2013. cbsnews.com
5. Denver Water, About us. denverwater.org/about-us
6. Thomas et al., tryptophan-like fluorescence as a fecal indicator method, manuscript under review at ES&T Water, 2026.
7. US EPA, Site-Specific Alternative Recreational Criteria Technical Support Materials for Alternative Indicators and Methods, EPA-820-R-14-011, December 2014. epa.gov/wqc
8. City of Boulder, E. coli in Boulder Creek. bouldercolorado.gov/e-coli-boulder-creek
9. Colorado Water Quality Control Commission, Policy 25-1, Advancing External Proposals, adopted 12 May 2025.
10. Colorado Newsline, "Colorado Gov.-elect Phil Weiser names transition team," 4 November 2026. newsfromthestates.com
11. Open Water Quality, global surface-water fecal indicator monitoring sites compiled from public sources; Colorado sites from the Water Quality Portal (EPA, USGS, NWQMC), extracted 10 November 2026. openwaterquality.org
12. Pierson, M., Fankhauser, K., Mehrabi, Z. (2026). Mapping waterways worldwide with deep learning. arXiv:2412.00050. Data: Fika and Better Planet Laboratory, WaterNet global waterways, Source Cooperative, doi:10.60480/a3sb-an07, CC BY 4.0. source.coop/fika/waternet
13. Colorado General Assembly, SB24-037, Study Green Infrastructure for Water Quality Management. leg.colorado.gov/bills/sb24-037
14. Landon, T., Johnson, A., Thomas, E. (2026). Applying water quality trading experience to Colorado Senate Bill 24-037. Journal of the American Water Resources Association 62(3), e70136. doi:10.1111/1752-1688.70136
15. Demaree, K., Johnson, A., Andersson, K., Thomas, E. A. (2025). The nature-based paradigm shift: identifying and overcoming barriers to sustainable water quality solutions. ACS ES&T Water 5(6), 2945-2952. doi:10.1021/acsestwater.4c01053