After checking the usual, Salinity, Nitrate and Phosphates. You should be checking Magnesium, Alkalinity and Calcium. These three parameters are very important when keeping short polyp stony,and long polyp stony hard corals, SPS and LPS respectively.
So what effects will low magnesium have on your reef aquarium?
You will find it very difficult to maintain high alkalinity and calcium levels if magnesium is low.
Corals will slow in growth and will cause some corals such as Duncans and torch corals to recede, and in some cases die. You may as many other reefers do, think you have something unseen and/or unheard of eating your corals, because branching heads or receding one by one. Don't get fooled by this, it more likely be the case of the weakest dies first as normally the case in nature. Confirm this by checking the level of Magnesium in your aquarium or even better have a list of checks to be carried out on set days.
So what should you do?
If you haven't already, go out and invest in a magnesium test kit and confirm that magnesium levels are low. Then simply use a buffer such as Seachem Magnesium buffer. Be sure to follow the instructions and don't overdose. Like everything in this hobby, do it very slowly. You will most definitely notice an improvement in a matter of days in the appearance of your corals.
As soon as you have adjusted your magnesium level to between 1200ppm and 1400ppm you should then work out the consumption rate of magnesium from your aquarium. This is simply done by checking magnesium over two to three days. For example check Monday and then Wednesday, if your Magnesium as dropped by 30ppm then it is safe to say that your aquarium is consuming 10ppm per day. At this low level in this example i would say it would be safe to adjust once every five days. If consumption is higher i would try and dose daily or every other day.
This is a simple guide and technology advances and chemical advances offer procedures such as dosing pumps and balling lite, these methods can be learnt with experience into this amazing hobby.