If it's the Vortech water to air kit, then it pipes the hot blower exhaust gasses through a heat exchanger and removes heat from those gasses by using the cooler water and heat absorbtion capabilty to cool the blower discharge air before it gets into the intake.
Any time air is compressed it makes heat as a byproduct. It makes no difference if it is a turbocharger, centrifugal supercharger or Roots type supercharger. They all heat the air as they compress it.
Heated air has two effects on engine operation:
1.) It reduces the power output because it is less dense that cold air at the same pressure. Denser air = more power.
2.) It increases the probability that detonation (spontaneous uncontrolled ignition of the air fuel charge) will occur and damage the engine.
Engines that operate with a hot intake air charge usually reduce the amount of spark advance. This reduces the odds that detonation will occur. It also reduces the power output.
So along comes the aftercooler or intercooler. Both are placed between the compressor and the intake valve and cool the intake air charge. This increases the air density and makes it possible to run more spark advance, both of which enable the engine to produce more power.
Aftercoolers or intercoolers come in two flavors: Air to air, or air to water. Both are similar to a mini radiator or heat exchanger in operation.
In an air to air intercooler, cooler air from the outside flows over the fins on the heat exchanger to cool the hot air inside. In theory, air to air intercoolers are limited to cooling the air to within several degrees of the outside air temp. In practice, this level of efficiency seldom happens: it is always 10 degrees or more hotter inside the intercooler than on the outside. The hotter the temp outside, the less temperature drop of the air charge inside the intercooler.
A variation of the air to air intercooler uses a burst of CO2 to cool the outside air flowing around the intercooler. Anyone who has ever used a CO2 fire extinguisher to cool the canned beverage of their choice can tell you how very effective this is. There is an obvious limitation since the pressurized CO2 takes up space and adds weight. The time duration of the effect is limited by the volume of the CO2 charge.
In an air to water intercooler, water flows over the outside of the heat exchanger to cool the hot air inside. Air to water intercoolers have an advantage in that they are more efficient for short time usage like a drag race. Chilled water can be used to make a greater temperature drop of the air before it gets to the intake valve. Air to water intercoolers have a limit on how long they can maintain this effect, since the hot air flowing through the intercooler gradually heats the water. That means you must either have a big tank of cool (or cold) water or the water will heat up to within several degrees of the air inside the intercooler.