Cryptosporidium and Giardia in Tap Water: Risks, Rules and Protection

Cryptosporidium (“Crypto”) and Giardia are microscopic parasites that can get into drinking water from human or animal feces. Both cause diarrheal illness. Crypto is the bigger concern for tap water because it is extremely tolerant of chlorine, the disinfectant most utilities rely on. That is why water systems that use rivers, lakes and reservoirs must also filter or use other treatment that removes or inactivates it. For most healthy people, an infection is unpleasant but short. For people with weakened immune systems, it can be serious. If your utility issues a boil water advisory, a rolling boil for 1 minute kills both.

What Crypto and Giardia are

Cryptosporidium is a parasite that causes cryptosporidiosis. The CDC calls it the leading cause of waterborne disease in the US. The most common symptom is watery diarrhea, though some people have no symptoms. Symptoms usually start 2 to 10 days after infection (about 7 days on average) and last 1 to 2 weeks. Most people with healthy immune systems recover without treatment.

Giardia is a gut parasite. The CDC says more people in the US get sick from Giardia than from any other gut parasite, and that swallowing just a few Giardia germs can make you sick. It can survive outside the body for weeks to months. Symptoms include diarrhea, gas, greasy stools that can float, stomach cramps, nausea and fatigue. They usually start 1 to 2 weeks after infection and last 2 to 6 weeks, occasionally longer.

Both spread when people swallow something contaminated with infected feces: water, food, soil or surfaces. Drinking water becomes a risk when feces from infected people or animals reach the river, lake, reservoir or well that supplies it, and treatment does not remove or inactivate the parasites.

Why chlorine is not enough

Chlorine kills most bacteria and viruses well. Crypto is different. CDC surveillance reports describe it as extremely chlorine-tolerant, which makes it well suited to spreading through treated drinking water and swimming pools.

So utilities rely on other barriers:

Filtration, which physically removes Crypto oocysts and Giardia cysts.
Ultraviolet (UV) light, which EPA says can inactivate Crypto and Giardia at lower doses than it needs for viruses.
Other options such as ozone and membrane filtration.

Turbidity (cloudiness) matters too. EPA notes that higher turbidity is often linked with higher levels of disease-causing organisms. For conventional and direct filtration plants, treated water turbidity can never exceed 1 NTU, a measure of cloudiness.

The 1993 Milwaukee outbreak

In March and April 1993, an estimated 403,000 people in the Milwaukee area had diarrheal illness caused by Crypto. The CDC called it the largest documented waterborne disease outbreak in the US since record keeping began in 1920.

A 1994 study in the New England Journal of Medicine traced it to one of the city’s two treatment plants. Treated water from the southern plant showed marked increases in turbidity from March 23 until April 9, when the plant was shut down, and the researchers concluded that Crypto oocysts had passed through its filtration system. According to the CDC, the treated water met all state and federal standards in effect at the time. The CDC also noted the utility would not have met the stricter turbidity standards that took effect later.

A follow-up study in the American Journal of Public Health (1997) found 54 deaths in the roughly two years after the outbreak that listed cryptosporidiosis as an underlying or contributing cause. About 85% of those people had AIDS listed as the underlying cause of death. This showed how dangerous Crypto can be for people with weakened immune systems.

How federal rules control Crypto and Giardia

EPA sets a health goal (MCLG) of zero for both parasites. Instead of a numeric limit, it uses treatment technique requirements, which apply to systems using surface water or groundwater under the direct influence of surface water:

Rule	Year	What it does
Surface Water Treatment Rule	June 1989	Requires 99.9% removal or inactivation of Giardia
Interim Enhanced SWTR	December 1998	Sets a zero MCLG for Crypto and requires 99% (2-log) Crypto removal for filtered systems serving 10,000 or more people
Long Term 1 Enhanced SWTR	2002	Extends the 2-log Crypto requirement to filtered systems serving fewer than 10,000
Long Term 2 Enhanced SWTR (LT2)	January 2006	Adds treatment based on the Crypto risk in each system’s source water

What LT2 added

The LT2 rule, published January 5, 2006, was built around the idea that some source waters carry much more Crypto than others. It requires:

Source water monitoring for Crypto, E. coli and turbidity.
Risk “bins.” Filtered systems are placed in one of four bins based on Crypto levels in their source water. Systems in higher bins must add treatment from a “microbial toolbox,” which includes UV disinfection and membrane filtration.
Inactivation for unfiltered systems, which treat source water without filtering it.
Covering or treating uncovered finished water storage, such as open reservoirs holding treated water.

Treatment violations in large US systems

A treatment technique violation under these rules means a system did not meet a required treatment or performance step. It is not a finding that Crypto or Giardia was detected in tap water.

We checked the 1,000 large systems on our site (each serving roughly 50,000 people or more). Source: EPA ECHO compliance records, checked October 7, 2026; last 12 quarters.

23 systems, serving about 16.3 million people, have a treatment technique violation under one of the surface water treatment rules. Sixteen are listed as still open.
7 of those have an LT2 treatment technique violation:

System	State	People served	Start date	Status
New York City System	NY	8,271,000	Feb. 2017	Open
Portland Water Bureau	OR	666,200	Dec. 2017	Open
Syracuse City	NY	192,000	Jan. 2024	Open
Monroe Water System	LA	57,000	Jan. 2026	Open
City of Asheville	NC	157,431	Oct. 2024	Closed
Reading Area Water Authority	PA	95,100	April 2025	Closed
Altoona Water Authority	PA	62,500	March 2026	Closed

Our data does not say which LT2 requirement was involved. Check each system’s EPA report or ask the utility. For more, see EPA serious violators explained and the states ranked by violations.

Note: utilities may have resolved issues since October 7, 2026. Check each utility’s EPA ECHO report or its latest Consumer Confidence Report for current status.

Who is most at risk

Anyone can get sick, but the CDC says people with weakened immune systems are more likely to get sick from germs in water. For Crypto, the CDC’s higher-risk groups include people with HIV, cancer and transplant patients taking drugs that weaken the immune system, and people with inherited immune disorders. In these groups, Crypto can cause severe, long-lasting illness and serious problems absorbing nutrients. The CDC also says children are more likely to get sick from Giardia.

If you are in a higher-risk group, the CDC advises talking with your healthcare provider about whether to treat your tap water and how.

How to protect yourself

During a boil water advisory

The CDC says to bring clear water to a rolling boil for 1 minute (3 minutes above 6,500 feet), then let it cool. Use boiled or bottled water for drinking, cooking, brushing teeth, ice and baby formula, and boil tap water even if it is filtered. Our boil water advisory guide covers the details.

Boiling is the surest way to kill parasites, bacteria and viruses. It does not remove chemicals.

Choosing a filter for cysts

If you want ongoing protection, for example because you have a weakened immune system, the CDC lists these options for removing parasites like Crypto:

Filters certified to NSF/ANSI Standard 53 or 58 for “cyst reduction” or “cyst removal”
Filters with an absolute pore size of 1 micron or smaller
Reverse osmosis, microfiltration, ultrafiltration or nanofiltration

A few cautions:

Check the claim, not just the standard. A filter certified to NSF/ANSI 53 for lead is not necessarily certified for cysts. The listing must say “cyst reduction” or “cyst removal.”
“Absolute” and “nominal” ratings are different. A “nominal” 1-micron rating does not mean the filter reliably stops particles that size.
Verify the exact model in the certifier’s online listing (NSF, IAPMO, WQA, CSA or UL) before buying. See our NSF certifications guide.
Change cartridges on schedule. The CDC advises people with weakened immune systems not to change filters themselves, since used filters hold the germs they trapped.

Our comparison of reverse osmosis and carbon filters explains how the main filter types differ.

Other everyday steps

The CDC recommends washing hands with soap and water, especially after using the toilet or changing diapers, avoiding swallowing water when swimming, and boiling or filtering water from lakes, rivers or springs before drinking it.

Bottom line

Crypto and Giardia are why surface water utilities filter and use treatment beyond chlorine. Large US outbreaks are rare today, but treatment lapses still happen. Check your system’s record on our search page, follow any boil advisory until it is lifted, and if your immune system is weakened, ask your doctor about a filter certified for cyst reduction.