Department of Environmental Quality
San Juan River health advisory: floodwaters recede, but E. coli levels surge
San Juan County-Utah, Nov. 6, 2026 – The highest flood surge moved through Montezuma Creek and Bluff on Wednesday and Thursday, meaning the worst of the active flooding has passed and river levels are starting to stabilize. Even with water levels dropping in many areas, however, serious hazards remain. Riverbanks are soaked through and at high risk of collapsing, heavy debris remains scattered throughout the area, and surface water and mud can remain dangerously contaminated with waterborne pathogens.
Mud and soil left behind after flooding remain contaminated because waterborne pathogens can survive in the ground for months. Exact survival times vary greatly and are hard to predict, as they are based on many environmental factors, but general estimates from the CDC suggest these pathogens take about two to three months to die off. Because of this, residents must be extremely careful around mud and soil in previously flooded zones, and anyone who comes into contact with these surfaces should wash their hands thoroughly and practice strict personal hygiene.
Drinking water
Public drinking water systems remain safe to use. Local municipal supplies do not pull water from the San Juan River and have not been affected by recent floodwaters.
Additionally, the hauled water being trucked to affected residents comes from a local groundwater well in Mexican Hat, which operates independently of the river system and remains unaffected by the flooding. Water hauling operations are expected to continue for the next one to two weeks.
Field technicians will continue testing water twice a week and will share updates every Friday. Testing for the drinking water in Montezuma Creek is set to take place on Monday.
If your private well was flooded or is located near recent floodwaters, you can have your water tested. While field technicians will collect samples for free, there is a $35 laboratory analysis fee. To request well sampling, contact Bluff Town Manager Erin Nelson at manager@townofbluffutah.gov or (435) 672-9990.
River E. coli levels
The latest laboratory tests for the San Juan River confirm that E. coli levels have increased significantly across several locations:
Mainstem San Juan River (Swinging Bridge, Sand Island, and Mexican Hat): All collected samples reached the upper detection limit of the laboratory assay, exceeding >2,419 MPN/100mL. Samples collected Wednesday afternoon at Mexican Hat during high flows (~21,000 cfs) mirrored these elevated levels.
South Cottonwood Wash: Inflow samples measured between 435 MPN/100mL and 579 MPN/100mL. While these readings are lower than the mainstem river, they remain more than double the threshold established for safe recreational contact.
Waterborne pathogens in the river have spiked because flooding compromised sewer lagoons upstream in Pagosa Springs, Farmington, and Montezuma Creek, causing untreated sewage to spill into the waterway. Last week’s flooding also damaged septic systems and stirred up large amounts of mud and debris.
Safety guidelines
Stay completely out of the river until further notice. Because the water poses serious health risks, do not swim, wade, boat, or allow animals to wade in or drink from it. We will continue to release updated guidance as testing continues.
