One area of ongoing experimentation by aquarists is the refugium photoperiod. To date, no one has proven that a particular refugium lighting regimen is ideal, at least for all systems. Fortunately, it doesn’t seem like any are harmful! Planted refugia seem to “work” just fine as long as they receive at least ten or twelve hours of intense light per day. Still, some aquarists run their lights 24 hours/day without any apparent ill effect.
One method that is well worth mention here, though, uses a so-called reverse photoperiod. The “reverse” part comes from the fact that the refugium lights are timed to operate “on” while the main tank’s lights are “off,” and vice-versa. The reason for this is that it balances (at least in theory) water chemistry deviation that occurs as a result of the photosynthetic activity of the plant life, both in the main tank and in the fuge.
As you very well may know, plants (including macroalgae) take up carbon dioxide from their environment in order to store energy (i.e. make sugar) as well as to build biomass. Drawing carbon dioxide from water alters the carbonic acid balance such that it raises pH. Plants only do this while carrying out photosynthesis. The result is that (especially in a small, closed system like an aquarium) sharp pH swings can occur between day and night cycles.
In a reef tank loaded with hermatypic corals and clams, you might have a lot of photosynthetic activity happening during the “lights on” cycle; activity in the refugium can add to this if its lights run “on” concurrently. However, if its lights are on alternately, the refugium can perform a beneficial balancing act by stabilizing diurnal (i.e. day/night) pH values!
We only strongly suggest one thing; no matter what light cycle you choose, be sure to use timers because, with macros, consistency is certainly key to their health!