This is a very complex question, but I will try to answer as simply as possible.

Since you are from San Juan County NM I will assume that you use water to irrigate the produce not just to wash it after harvest. According to a Penn State University Extension publication (http://extension.psu.edu/food/safety/farm/gaps/safe-uses-of-agricultural-water) the Environmental Protection Agency has determined safe levels of E. coli allowed in irrigation water for produce. Contact your local water company or health department to find out what the levels are in your water and how they compare to these safe irrigation water standards. The health department may also have information on safe practices, based on the current contamination level.

Another good resource could be the New Mexico Environmental Department (https://www.env.nm.gov/dwb/Safe/boil_water_orders2.htm) Their website indicates boil advisories in your county. They should have more information on what the levels of contamination are as well as if the water, depending on its source, is safe for horticultural use. Their contact information is in the top right corner of this website. This site will also inform you when there is a boil water advisory and when the current one will be lifted.

Produce can become contaminated in three ways: from direct contact of contaminated water on the tomato or other food item (surface contamination), absorption of contaminants through the skin of the produce, and absorption into the cellular structure of the produce through the roots, etc. Surface contamination could also occur if produce touches the ground that has been sprayed with contaminated water. A University of Florida Extension publication (http://edis.ifas.ufl.edu/pdffiles/SS/SS48400.pdf) reports:

“Laboratory studies using high doses of bacteria suggest that Salmonella and E. coli O157:H7 contaminate produce in the field by colonizing plant-root surfaces from infested soil or seeds. Bacteria then spread to all parts of the plant (9).”

In all cases, the level of water contamination will need to be determined to know if the water is safe to use on the plants/produce or not.

If the level of E coli in the water is above the recommended safe levels mentioned abovetoo contaminated, the vegetables could potentially be cooked to destroy the contaminants. However, you should be very careful to handle such produce carefully and wash your hands thoroughly after handling them and possibly wear gloves when harvesting and handling such produce.  But it is really better to be safe than sorry and if in doubt, throw the produce out.

If it turns out that produce consumption is allowable, it is always advisable to wash produce (including tomatoes, peppers and all that you mention in your question) before eating them. This should be done with clean water which means the contaminated water would need to be boiled and cooled to within 10 degrees Fahrenheit of produce temperature before washing the produce. This reduces the risk of absorption of contaminants during the washing process. Likewise, thick-skinned produce should also always be washed before eating (if it is deemed fit to consume in this situation). Melons and cantaloupe can be washed, scrubbing well to make sure surfaces are clean. Even though the skin or rind is not eaten, any contaminants left on the outside will enter and contaminate the flesh that is eaten when the fruit is cut. Also wash hands and sanitize surfaces and utensils that touch contaminated produce.

Another resource is Dr. Nancy Flores, Food Technology Specialist with New Mexico State University Extension. Her contact information can be found at http://efcs.nmsu.edu/food-technology.html.

Thank you for using the Ask an Expert feature of eXtension.org. If I can be of further assistance, please feel free to ask.

Thank you for your response. It helped me a lot and i now know who to contact. 

Thank you,

Michele Pusch