I look to RHF for all reef chemistry questions. This should help your understanding:
http://www.advancedaquarist.com/2002/5/chemistry
Here's the applicable part of the rather dense reading:
pH vs. Alkalinity in Reef Tanks
At the start of the last section, it was pointed out that "_there is an exact mathematical relationship between pH and carbonate alkalinity for any aqueous system in equilibrium with the atmosphere_". An important point to keep in mind is that the relationship will be altered slightly if the tank is not in equilibrium with the air. Specifically, reef tanks are often not in equilibrium with the air, making the internal pCO2 for the tank something different than the surrounding air.
For example, tanks using limewater can have a pH value of 8.5 with a total alkalinity of only 3 meq/L. Looking at Figure 2, this puts them off of the theoretical relationship for seawater in ambient air. The fundamental explanation is that the tank is deficient in CO2. In effect, the tank has an internal pCO2 that is more like that for the preindustrial air with 273 ppm CO2 (Figure 2). In this case, driving more CO2 from "normal air" into the water would lower the pH to about 8.2-8.3 while maintaining the same alkalinity.
Likewise, tanks that use calcium carbonate/carbon dioxide reactors often have a pH of 8.0 with an alkalinity of 3 meq/L (or more). Again, that set of values falls off of the theoretical curve shown in Figure 2. In this case, the tank has an artificially high internal pCO2 of more than twice "normal air". Driving more CO2 from the tank into "normal air" would raise the pH to about 8.2-8.3 while maintaining the same alkalinity.
A third way that reef tanks can present unusual combinations of pH and alkalinity is if the tank is in an environment where the ambient CO2 is far from normal. Rarely would such a situation involve reduced CO2, but homes and businesses are frequently elevated with respect to CO2. Such levels as those represented by the 700-ppm line in Figure 2 are frequently encountered by aquarists, especially those living in newer, "tighter" homes (and some have proven this fact to themselves with carbon dioxide detectors). Aquarists that experience chronic low pH despite adequate alkalinity and aeration may do so because their homes have such elevated levels of carbon dioxide. Many of these aquarists have found that the pH of their tanks rises substantially by simply leaving a window near the tank open to permit better exchange with exterior, "normal" air.
