The efficiency of gas heaters has improved considerably over the years and today a typical gas pool heater is between 80% and 85% efficient (a good example is the Jandy Legacy heater). This means that this percentage of the energy consumed is transferred to the pool water. The remainder is lost in various ways, mainly through discharge into the atmosphere.
However, much higher efficiencies are possible. The Jandy Hi-E2 has an amazing energy efficiency rating of 95% and you may wonder why all gas pool heaters cannot offer this level of performance.
Well there is a negative side to high efficiency gas heaters and this is reflected in the price of this Jandy model which is significantly higher than other similar models.
At the 80-85% range the wasted energy actually provides a useful function and allows the heater to operate in a simple way. The products of combustion within the heater are principally carbon dioxide, carbon monoxide and water vapor and these must be discharged safely. The unused heat exits through the stack and in doing so provides lift for the waste gases and allows them to be efficiently discharged.
As the efficiency of the heater increases there is less unused heat and the waste gases are less efficiently discharged. At a certain point this process is no longer effective and condensation occurs within the stack. The result (called the condensate) is acidic which means that more expensive, corrosion resistant, materials have to be used and fans need to be installed to vent the gases properly. In addition the condensate must be collected and disposed of safely. All of this increases the cost of the heater and its installation.
Whilst high efficiency gas heaters are often appropriate for a commercial installations it is unlikely that they will be cost effective in a residential situation. Here the heater is not likely to be used enough for the increased efficiency to offset the higher price.
It is noted elsewhere on this site that the advantage of gas heaters is that they can quickly heat up a pool but where a pool is heated constantly a heat pump is a better option. This would indicate a limited market for high efficiency gas pool heaters.