The Water That Rinses the Scope: How Contaminated Rinse Water Spreads Endoscope Infections

There is a quiet assumption behind every endoscopy: that whatever was used to clean the scope left it cleaner than it found it. Usually that is true. But cleaning a flexible endoscope ends with a rinse to flush the chemical disinfectant back out of the channels, and that rinse uses water. If the water carries bacteria — and hospital water systems routinely do — the last thing to touch the inside of the scope before it goes into the next patient can be the thing that contaminates it. This is not a fringe theory. It is why the reprocessing standards that govern American hospitals treat water as a controlled input, and why, when a serious infection follows a scope procedure, the water-quality records are among the first documents worth pulling.

The Last Step in Cleaning a Scope Is a Rinse — and the Water Isn’t Sterile

Reprocessing a reusable endoscope runs through a set sequence: bedside pre-cleaning, manual brushing and flushing, then high-level disinfection (usually inside an automated endoscope reprocessor, or AER), and finally one or more water rinses to remove the disinfectant chemicals so they do not injure the next patient. That final rinse is unavoidable — you cannot leave glutaraldehyde or peracetic acid inside a scope. But ordinary tap water is not sterile. Municipal and building plumbing routinely contain low levels of bacteria, and certain organisms actively thrive in water systems. When the rinse water is contaminated, the final step designed to make a scope safe can instead reseed it with bacteria after disinfection has already been done.

The organisms of greatest concern are the ones built for water. Pseudomonas aeruginosa is the classic waterborne hospital pathogen; nontuberculous (environmental) mycobacteria and Legionella pneumophila are others. Infection-control specialists call these opportunistic premise plumbing pathogens — microbes that live in the biofilm coating the inside of pipes, tanks, and tubing, tolerate low disinfectant levels, and are perfectly positioned to ride a water rinse into a medical device. The same “high-concern” organisms the FDA flags for duodenoscopes, including Pseudomonas, overlap heavily with the ones that colonize water.

How Contaminated Rinse Water Actually Causes an Infection

The mechanism is straightforward and, unfortunately, efficient. A scope is disinfected, then rinsed with water carrying Pseudomonas or mycobacteria. Some of those organisms are left behind in the long, narrow, hard-to-dry channels. If the scope is then stored damp — another documented reprocessing failure we cover in our piece on what borescope inspections reveal about “clean” scopes — the retained moisture lets the surviving bacteria multiply overnight and form biofilm. The next patient is then examined with a scope that is microbiologically dirtier than it was when it came off the last one. The water did not just fail to clean; it delivered the contamination.

The water lines inside the reprocessor are a second hiding place. A 2026 study in Scientific Reports traced microbiological non-compliance of endoscope final-rinse water to opportunistic premise plumbing pathogens colonizing the connecting tubing of the reprocessing equipment itself — meaning the machine built to clean the scope had become a reservoir feeding contamination into the rinse. This is why the standards do not stop at “use clean water”; they reach the filters, the tubing, and the maintenance of the water system that supplies the AER.

What the Standards Require: ANSI/AAMI ST91 and ST108

Two national consensus standards set the reprocessing standard of care in U.S. hospitals. ANSI/AAMI ST91:2021, the standard for flexible and semi-rigid endoscope processing, addresses the microbial quality of rinse water directly and calls for testing the water in automated endoscope reprocessors specifically so that a contaminated final rinse does not recontaminate the device. ST91 classifies duodenoscopes, linear ultrasound endoscopes, bronchoscopes, and ureteroscopes as high-risk endoscopes warranting the most rigorous handling — the same devices at the center of the urological-scope and duodenoscope infection cases.

For the water specifications themselves, ST91 now points to ANSI/AAMI ST108:2023, Water for the Processing of Medical Devices. ST108 replaced the older technical report TIR34 and defines categories of water by how it is used: utility water for washing and intermediate rinsing, and critical water — the higher-purity, treated water — for the final rinse. It identifies roughly a dozen water impurities that facilities are expected to control and calls for testing at both the point where the water is generated and the point where it is used. In plain terms: the final rinse is supposed to use treated, monitored water, not whatever comes out of the tap.

On the monitoring side, the Healthcare Infection Society (HIS) Working Party, in a 2022 report in the Journal of Hospital Infection, recommended checking final-rinse water for total viable bacterial counts weekly and for Pseudomonas aeruginosa and environmental mycobacteria quarterly, and concluded that rinse water should be free of waterborne pathogens such as P. aeruginosa, environmental mycobacteria, and Legionella pneumophila. The Working Party treated final-rinse water in the range of 10–100 colony-forming units per 100 mL as unsatisfactory for reprocessing high-risk endoscopes. Reverse-osmosis treatment with routine monitoring is the approach shown to keep those pathogens out; a five-year study of reverse-osmosis-fed endoscopy units published in the same literature reported no Pseudomonas, environmental mycobacteria, or Legionella isolated over the entire period. Clean water is achievable — when the system is built and maintained to deliver it.

The Documented Water Outbreaks

The clearest illustration comes from a documented outbreak summarized in the HIS Working Party report: 23 patients were infected with Pseudomonas aeruginosa after cystoscopy at a facility where the scopes were processed manually and the breaches included changing the final rinse water infrequently and using tap water for the final rinse. The device was not the villain in that story — the water and the process were. It is a concrete example of a pattern the standards exist to prevent: skip the treated water, skip the monitoring, and a common plumbing organism becomes an outbreak.

It also reframes how to read a post-procedure infection. When the organism cultured from a patient is a textbook waterborne pathogen — Pseudomonas, a nontuberculous mycobacterium, Legionella — that is a clinical signal pointing toward the water and the reprocessing system, not away from them. We walk through the broader set of these signals in signs a scope, not chance, caused your infection, and how the causation science works in proving a scope caused an infection.

Why Rinse-Water Quality Matters to a Scope-Infection Case

A scope-infection claim generally runs on two tracks. One is product liability against a manufacturer — whether a device was designed or sold in a way that makes reliable cleaning unrealistic. The other is hospital reprocessing negligence — whether the facility followed the applicable cleaning, water-quality, drying, and monitoring steps. Rinse-water quality lives squarely on the second track, and it is one of the more provable failures because it leaves a documentary trail. Either the facility has the treated-water test results, the filter-change and reverse-osmosis maintenance logs, and the AER water-line records — or it does not.

That is the investigative value of the water angle: it converts a hard causation question into a records question. If a patient grew Pseudomonas after an ERCP, colonoscopy, or bronchoscopy, an investigation looks for the final-rinse water-test results around the date of the procedure, the maintenance history of the water-treatment system and the reprocessor, and the device-tracking log tying a specific scope to that patient. Where cultured organisms are preserved, DNA sequencing can compare the patient’s strain to organisms recovered from the water or the scope. These records exist, but they are kept on limited retention schedules and can be purged — which is why the guidance in our article on the evidence a scope-infection case needs is to move before the paper trail disappears.

A Trial Lawyer’s Read

“Everybody wants to argue about the scope, and sometimes the scope is the problem,” says Alex Alvarez, Managing Partner of The Alvarez Law Firm and a Board Certified Civil Trial Lawyer. “But I’ve learned to also ask a boring question: what water did you rinse it with, and can you prove it was clean? A hospital either hands me the treated-water test logs, the filter-maintenance records, and the reprocessor water-line results, or it can’t. When the records are there and they’re good, that closes a door honestly. When they’re missing, thin, or show they were skipping the monitoring, that tells me something the marketing brochure never will. The water leaves a paper trail, and paper trails are where cases are won or lost.”

The microbiology has to point the same direction as the records. “The organism itself is a clue,” notes Herb Borroto, M.D., J.D., the firm’s Medical-Legal Expert, who holds both a medical degree and a law degree. “Pseudomonas aeruginosa, environmental mycobacteria, Legionella — these are water organisms. When I see one of them in a patient who was fine before a scope procedure, I want the final-rinse water results, the reverse-osmosis and filter maintenance, and whether the facility was doing the weekly and quarterly testing the standards call for. Then I line that up against the timing and the cultures. My job is to say whether the documents support the connection or rule it out. If the water was tested and clean, I’ll say so. If it wasn’t, that’s a finding.”

What to Do Now

If you or a loved one developed a serious infection — a bloodstream infection, sepsis, a drug-resistant organism, or a waterborne pathogen such as Pseudomonas or a nontuberculous mycobacterium — in the days or weeks after a colonoscopy, ERCP, cystoscopy, or bronchoscopy, do not assume it was random simply because there was no outbreak in the news. Many of these are quiet, single-patient events, and the reprocessing and water-quality records that could connect a device to an infection are not kept forever. Knowing what to request, and how quickly, can be the difference between a preserved case and a lost one. Our infection symptoms page can help you recognize the warning signs worth taking seriously.

A short, no-obligation review can tell you whether the facts warrant pulling those records and whether a filing deadline may be approaching. We represent patients nationwide. Free case review. No Fees Unless We Recover Money for You.

Frequently Asked Questions

Can the water used to rinse an endoscope give you an infection?

Yes, it can. The final step in cleaning a flexible endoscope is a water rinse to remove disinfectant, and if that water is contaminated it can recontaminate a scope that just passed disinfection. Waterborne organisms such as Pseudomonas aeruginosa, nontuberculous (environmental) mycobacteria, and Legionella pneumophila live in plumbing and water systems and have been tied to endoscopy infections. The reprocessing standard ANSI/AAMI ST91:2021 specifically addresses the microbial quality of rinse water and the testing of water in automated endoscope reprocessors so the final rinse does not recontaminate the device. Most rinses are uneventful, but a serious infection after a scope procedure is a reason to ask whether the water was tested and treated as required.

What do ANSI/AAMI ST91 and ST108 require for endoscope rinse water?

ANSI/AAMI ST91:2021 is the U.S. standard for flexible and semi-rigid endoscope processing; it addresses the microbial quality of rinse water and calls for testing the water in automated endoscope reprocessors so a contaminated final rinse does not undo disinfection. For the water specifications themselves, ST91 now points to ANSI/AAMI ST108:2023, Water for the Processing of Medical Devices, which defines water categories — utility water for washing and intermediate rinses and critical water for the final rinse — controls roughly a dozen impurities, and calls for testing at the point of water generation and the point of use. Duodenoscopes, ultrasound endoscopes, bronchoscopes, and ureteroscopes are treated as high-risk devices under these standards.

Have contaminated-water outbreaks from endoscopes actually happened?

Yes. The infection-control literature summarized by the Healthcare Infection Society Working Party includes an outbreak in which 23 patients were infected with Pseudomonas aeruginosa after cystoscopy at a facility where scopes were processed manually with breaches that included changing the final rinse water infrequently and using tap water for the final rinse. More recent work has traced final-rinse-water contamination to opportunistic premise plumbing pathogens colonizing the connecting tubing of reprocessing equipment. These are the reason standards call for treated water, routine microbiological monitoring, and control of the water lines inside the reprocessor.

Why would rinse-water quality matter to a scope-infection lawsuit?

Because it can show whether a hospital met the reprocessing standard of care. A scope-infection claim often turns on hospital reprocessing negligence — whether the facility followed the applicable cleaning, water-quality, and monitoring steps. If the organism cultured from a patient is a classic waterborne pathogen such as Pseudomonas or a nontuberculous mycobacterium, an investigation looks for the facility’s final-rinse water-test results, the maintenance and filter-change records for its water treatment and automated endoscope reprocessor, and the device-tracking log tying a specific scope to the procedure. Those records exist but are kept on limited retention schedules, so preserving them early matters.

Sources

• Association for the Advancement of Medical Instrumentation — ANSI/AAMI ST91:2021, “Flexible and semi-rigid endoscope processing in health care facilities” (microbial quality of rinse water; testing of water in automated endoscope reprocessors; classification of duodenoscopes, ultrasound endoscopes, bronchoscopes, and ureteroscopes as high-risk). array.aami.org
• Association for the Advancement of Medical Instrumentation — ANSI/AAMI ST108:2023, “Water for the Processing of Medical Devices” (utility vs. critical water categories; control of water impurities; testing at point of generation and point of use; replaces TIR34). steris.com
• Walker JT, et al. “Final rinse water quality for flexible endoscopy to minimize the risk of post-endoscopic infection. Report from the Healthcare Infection Society Working Party.” Journal of Hospital Infection (2022) (weekly total-viable-count and quarterly Pseudomonas/mycobacteria monitoring; 10–100 CFU/100 mL unsatisfactory for high-risk endoscopes; waterborne pathogens of concern; documented cystoscopy outbreak of 23 P. aeruginosa infections). pubmed.ncbi.nlm.nih.gov
• “Investigation of microbiological non-compliance of endoscopic final rinse water associated with opportunistic premise plumbing pathogens contamination in connecting tube.” Scientific Reports (2026) (final-rinse-water contamination traced to plumbing pathogens in reprocessor connecting tubing). nature.com
• U.S. Food & Drug Administration — “Infections Associated with Reprocessed Duodenoscopes” and reprocessing communications (definition of “high concern” organisms including Pseudomonas aeruginosa; recognition that reusable flexible endoscopes can remain contaminated after reprocessing per the manufacturer’s instructions). fda.gov
• Centers for Disease Control and Prevention — Healthcare-Associated Infections; guidance on waterborne and opportunistic premise plumbing organisms (Pseudomonas aeruginosa, nontuberculous mycobacteria, Legionella) in health care water systems. cdc.gov

This article is for general informational purposes only and is not legal or medical advice. It summarizes published research, consensus reprocessing standards, public health guidance, and regulatory communications as of the publication date; standards and scientific methods can change, and this article does not describe the outcome of any client’s case. References to reprocessing failures and outbreaks describe published findings, not any individual’s claim. The existence of investigative methods such as water testing, culturing, and genetic typing is evidence to be evaluated on the facts, not proof of any individual’s claim. Nothing here creates an attorney-client relationship, and no result is promised or implied. Past results do not guarantee future outcomes. Deadlines and legal standards vary by state and by the facts of each case. If you believe you may have a claim, consult a licensed attorney promptly.