FWIW, I detail these issues with respect to ammonia and pH here:
Ammonia and the Reef Aquarium by Randy Holmes-Farley - Reefkeeping.com
http://reefkeeping.com/issues/2007-02/rhf/index.php
from it:
Figure 1. The fraction of free ammonia (NH3) and ammonium ion (NH4+) present in seawater as a function of pH.
Ammonia and Ammonium as a Function of pH
The pKa of ammonium in seawater is about 9.3 (some references state 9.5, with the difference possibly relating to the different pH scales sometimes used for seawater and freshwater).2 That pKa means that at pH 9.3 the water has equal concentrations of ammonium and ammonia. At pH values below this level, as is always the case in reef aquaria, ammonium predominates. Figure 1 shows a plot of the relative fractions of ammonia and ammonium as a function of pH in seawater. At pH 8.2 only about 7% of the ammonia is present as free ammonia, with 93% present as ammonium.
Because many authors attribute ammonia's toxicity primarily to free ammonia (whether this is correct or not, see below), Figure 2 shows an expanded view of Figure 1 for the free ammonia concentration over the pH range of usual interest in reef aquaria. The amount of free ammonia present at pH 7.8 is about one-fourth the amount present at pH 8.5.
Figure 2.The fraction of free ammonia (NH3) present in seawater as a function of pH over the range of most interest to reef aquarists. This figure reproduces Figure 1 on an expanded scale.
Reef aquarists also are often interested in pH values below those typically present in actual reef aquaria. A shipping bag containing fish, for example, often drops substantially in pH over the course of hours to days, as a result of expelled carbon dioxide. That change in pH can convert even more of the free ammonia to ammonium, and Figure 3 shows the fractions of ammonia and ammonium on a log scale, making it clear that the free ammonia continues to drop in concentration as the pH drops, even when it is already present as a very small fraction.
Figure 3.The fraction of free ammonia (NH3) and ammonium ion (NH4+) present in seawater as a function of pH. This figure shows the fraction on a log scale over a wider pH range than Figure 1.