There could be a lifeform (e.g. an algae or plankton) that filters salts out of the ocean that turns the salt products of an acid-base reaction back into the components. The lifeforms could "capture" the base, incorporating it into their body and protecting it from acid. This releases the acid back into the sea.
Apart from the salt itself, the organism would rely on two main things for this reaction: energy and hydrogen.
Since neutralisation reactions are exothermic (releases energy/heat), the inverse will be endothermic (requires energy). Thus you could expect the organisms to thrive particularly well around geothermal activity, and to live more slowly in smaller numbers on the surface (particularly in warm/sunny areas). Solar-adapted versions may have the ability to build a small "charge" from solar energy over time.
Hydrogen is needed to replace the base from the salt and turn it back into an acid. If they're in a water body, there's hydrogen in water (again, endothermic to split H20). This would release atomic or molecular oxygen into the water, which the organism or other organisms might use for respiration. This isn't a substitute for photosynthesis in the world, though; they're not splitting carbon dioxide.
So if we look at this, we have an organism that dwells on the surface and around geothermal activity, which captures bases from salts and keeps the ocean acidic. This will gradually erode the mineral landscape, but this may be a tectonically active planet. When the organisms die they may sink down and form protective layers (assuming however they hold the base safe from the acid is stable), preventing the acid from eating downwards.
So why are people living in places where these organisms live? Perhaps it's just because they want the same things - geothermal activity can provide uses for people, and often contributes to land fertility. Perhaps there are other dangerous organisms that the acidic seas keep at bay.
So, which chemicals??
Firstly, which salt? There'll be a few factors that make it more likely for this kind of organism to survive. The "lattice enthalpy" of a compound relates to the energy required to break the bonds, so different salts are more easily broken than others. I don't know if the organism would survive better with an easily ionised salt (because it takes less energy to break it) or a more strongly ionised one (because the bonds it forms by adding the molecules to its body are more stable). I don't know enough about chemistry to work out which salts have more or less lattice enthalpy!
Which acid? The stronger the acid, the harder it will be for the organism to store the base safely. However, a stronger acid will also react with other things faster (e.g. minerals in the landscape), forming food for the organisms. Because the organisms are limited in their "processing" by their intake energy, they might be more likely to have evolved with a medium-strength acid.
I'm no chemist or biologist, so I don't know which to recommend! Probably pick whichever's more suitable for the setting. Depending on the use of the setting you might not want to specify the acid or salt in question, and just describe the effect.