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I am not sure the order that the water travels through (I think it is neutralizer, softener, nitrate but am not sure). We do not add anything to the neutralizer, I was told that they add something to this once per year. We have 2 salt tanks, 1 for the nitrate tank and 1 for the softener.
I reported the elevated nitrates to the company that installed the filter and they came and set the backwash to once every 5 days rather than once per week... I am still using bottled water until we retest. They also replaced the timer on the neutralizer tank.
They said that the filters are resin tech? The softener tank is Challenger. The softener is 10x47 with a 155 control, the neutralizer is 10x54 with dome and 163 control, and the nitrate has a Logix control. We were told the softener has a big brine tank and the nitrate filter has a smaller brine tank.
I spoke with a separate company that said they fishy odor we originally had was likely from the resin of the new nitrate filter. They also said a reverse osmosis would be optimal and a combo softener/nitrate tank would have been better than the separate ones. He said the issue with low PH, high nitrates, and high manganese is since the wells here are shallow. He does not service this area, so while the information was great we are still trying to figure this all out.

Answer
Jenn,
You finally talked with someone who made some sense!  Too bad he doesn't serve your area!!   OK, here is my answer (finally, I know :-) I think I understand your system as good as I can without actually inspecting it (which, in this case, would have been my preference).  

Here is what I understand of your system:

Your raw well water is not drinkable in it's natural form due to two main factors: low pH and high nitrates.  There is also secondary concern from Manganese (<0.5ppm) and Iron (Fe)  (<3 ppm).  Neither the Manganese or the iron is present in levels that would be detrimental to human health.  The iron will cause fixture staining, clothing stains, etc. and is an aesthetic nuisance issue.   Read this article on Manganese (Mn)

http://www.epa.gov/safewater/ccl/pdfs/reg_determine1/support_cc1_magnese_dwrepor

The Fe/Mn contaminants are treated with ion exchange.  The low pH is treated with an acid neutralizer and the nitrates are treated with an ion exchange resin.  Read this article on Nitrate removal with ion exchange:

http://www.wwdmag.com/nitrate-removal-ion-exchange

Both the nitrate removal and the Fe/Mn treatment utilizes salt (NaCl) for the ion exchange.  It is unknown to me what type of resin is contained in the units as the company servicing this system is not forthcoming with information on their equipment.  They apparently have told the customer that they use "Backwash" to control the units.  I have never heard of this.   Most softeners are controlled by time of regeneration.  Backwash is related to regeneration in that it is one step but not the determining factor.  Resin will remove a certain amount of contaminant from the water that passes through it.  It replaces the nitrate or Mn or Fe with another ion (either Na or Cl).  When the resin is "full" it must be regenerated or water will pass through without having the contaminant removed.  So most systems controlled by the regeneration cycle.  You know how much contaminant is removed by the resin, how much resin is in the tank and by calculation you can figure how much raw water the unit can treat before it needs to be regenerated.  You usually put a water meter in the system and when x amount of water passes through it automatically starts a regeneration (and also backwash, etc.).  So controlling the system by backwash makes absolutely no sense!!  Here is a really good website on some basic water controls.  This is from a company that I have done some consulting for and is very reputable in the California area.

http://www.remco.com/ix-quest.htm#3

My recommendations are:
1. Get a reputable water treatment company to come out and inspect your system and make the necessary changes.
2. Look at installing a Reverse Osmosis (RO) system for treating drinking water.  You can install a very good RO system (installed after the current treatment) for under $500.  This will provide adequate and safe drinking water for your entire family.

Without any more information I am not sure what caused the fishy odor you experienced.  I would guess that you may get periodic incursions of hydrogen sulfide (H2S) in your well water.  Most systems where there is nitrate (NO4) and Mn contamination contain at least a little H2S.  The H2S has a very obnoxious fishy or rotten egg odor.  A backwash failure makes no sense to me.

So, if you have any questions please let me know.  If you want to contact me directly you can email me at: CarolinaWaterEngineering@roadrunner.com

Good luck,
Steve  

Water Quality

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Steve Young

Expertise

I will answer questions on residential water treatment, i.e. use of softeners, filters, reverse osmosis systems, disinfection, iron and/or sediment removal and other issues facing the homeowner. I have worked extensively with well water systems.

Experience

I have worked in the water treatment area for many years as a consultant and as a professional environmental engineer in the private industry sector. I have designed reverse osmosis, deionization, and water softening systems. I have also done work in water quality and stream and river remediation as it relates to the Clean Water Act.

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I am currently serving as an Expert for Home Improvement, Travel (New Mexico) and Travel (North Carolina);

Education/Credentials
BS Environmental Eng.

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