Chemical water treatment: Acid Base reaction I was thinking of a hypothetical waste system that uses nanotechnology to its advantage.

At the individual level, waste just passes through into pipes when flushed like it normally does.

But once it reaches the water treatment plant there is an initial filter to catch solid waste(in other words poop) and divert it to a different part of the system where it gets dried and eventually ground into a biosolid that can be used as fertilizer.

Meanwhile all the urine, vomitus, blood, and any diarrhea that didn't get caught by the initial filter is passed through a series of filters to catch smaller and smaller waste products from cells all the way to molecules like urea being blocked with a nanofilter. Only a few compounds besides water are left. Yes there are still small ions like potassium and this might actually pose a problem.

But the real threat is that $\ce{HCl}$ is still in the water. Pepsin and other enzymes have been blocked by the nanofilters but $\ce{HCl}$ is still small enough to pass through all of the filters. A nanofilter that can block $\ce{HCl}$ is so impractical that it would most likely block the water itself until either the water treatment system or the microfilters and nanofilters burst from pressure and you end up with a critical failure either way.

So there has to be a chemical reaction that either deactivates the $\ce{HCl}$ and thus renders it harmless or a reaction that leaves no trace of $\ce{HCl}$.

I was thinking that to render the water safe, $\ce{NaOH}$ should be added to increase the amount of saltwater and totally get rid of the $\ce{HCl}$. But then I realized that with potassium and other ions besides sodium and chloride still in the water this could make the water toxic due to toxic salts forming.

Potassium chloride is the least harmful of all the salts that could form besides sodium chloride. Other than the bitter taste, there is basically nothing wrong with using potassium chloride. Similar for calcium chloride. Magnesium chloride though could cause diarrhea due to the magnesium(I know at least part of that diarrhea is from magnesium because the magnesium supplement I take helps to prevent constipation). I am not as worried about hydroxides because those would react with hydrogen ions to produce water.

But those salts are not the only problem. The other problem is how much $\ce{NaOH}$ to add.

I mean to get $\ce{HCl}$ down to 0 every time, there would have to be sensors to not only know the volume of water but also the concentration of $\ce{HCl}$ and a relatively complicated math problem like this:

$$[\ce{HCl}] * x = a mol \ce{HCl} = a mol \ce{NaOH} = [\ce{NaOH}] * y$$

What is complicated about it? Well for one how would you sense the exact concentration of a strong acid or base without damaging the sensory equipment? And unless you regularly go to the water treatment plant with this nanotechnology, you won't know what the concentration of $\ce{NaOH}$ is. And the concentration of $\ce{HCl}$ will most likely vary day to day depending on factors such as these:


How often any given person vomits
Hydration level before vomiting
Amount of bile in the vomit
Dilution of stomach acid
Amount of blood in the vomit if any
Prevalence of vomiting from any cause
Total Volume of vomit


So basically my question is how can I have the part of the system after the filters be constantly sensing the exact concentration of $\ce{HCl}$, doing the math, and adding the amount of $\ce{NaOH}$ that will get the concentration of $\ce{HCl}$ down to exactly 0?
The question is long and detailed, and deserves a long answer, but I can only hit on the highlights, and urge others with some expertise in this area (which I lack) to weigh in.

First, the science of water treatment is mature and has addressed many of the issues raised here, primarily through biological and chemical processes which are very good at breaking down and dissolving most of the different sized particles you refer to. 

As far as the composition of sewage is concerned it contains a lot more water than human waste, and a lot more normal waste (urine and fecal matter) than vomit, which, since most people are sick only a tiny fraction of their lives, and nauseous an even smaller fraction, likely is a vanishingly small contributor to the content of sewage. The composition of sewage at the treatment plant intake varies much less, and more slowly, than you might think, since it is averaging the inputs from people all over a city or region. Still, it may vary seasonally due to changes in temperature or water usage, so the treatment must vary accordingly, as you have surmised.

Finally, you concern about neutralizing every last iota of HCl is misplaced. Adjustment of pH is commonly used in sewage treatment and is done using automated equipment and pH sensors that can withstand extended exposure to sewage and to pH fluctuations. The glass membrane electrode is a workhorse that is stable to extremes of pH well beyond what would occur in sewage.

But I conclude my answer by saying that some of your ideas are very interesting, and there may be many applications of nanotechnology in water treatment along the lines you mentioned, that could have practical benefits for peoples' lives. I urge you to continue your studies of wastewater chemistry with your full vigor and an open mind.