This is something that may seem small, but it bothers me … I mean really, really bothers me. The following issue will be expressed through the Brønsted-Lowry theory of acids and bases and specifically through the neutralistaion reaction of ammonia and hydrochloric acid. When I dissolve hydrochloric acid in water, the following equilibrium reaction takes place: $$\ce{HCl + H2O <=> Cl- + H3O+}\tag{1}$$ When I then add a base such as ammonia, $\ce{NH3}$: $$\ce{NH3 + H3O+ <=> H2O + NH4+}\tag{2}$$ Adding these 2 equations should give: $$\ce{NH3 + HCl <=> NH4Cl}\tag{3}$$
This implies that the first reaction produces hydroxonium ions which the second reaction uses up, hence the number of hydroxonium ions in the solution should remain the same as before the addition of the hydrochloric acid.
Now let's actually asses the implications of such a procedure. First of all, assume that the reaction has gone to completion. This implies that when I mix water with hydrochloric acid, I will get hydroxonium and chloride ions produced. Subsequently, when I add the same number of moles of ammonia as hydrochloric acid, this will react with all of the hydroxonium ions present in the solution, as is shown in reaction (2). One problem though; this isn't a full reaction. If I add the same number of moles of ammonia as hydrochloric acid, this time there will be more hydroxonium ions than there were in the solution before addition of the hydrogen chloride (this what what I guess will happen, and this is the center of my problem). So how do I become sure that the hydroxonium ions cancel out when the equations are added?