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I am not trying to write a comprehensive guide; I am merely trying to start a discussion on the subject.
If you can identify a parasite or other types of pests, treatments for those are debated in many great threads. The discussion in this post is more directed to the situations where the cause of the problem is unknown. We see many people asking for help to troubleshoot systems that are not thriving, and we frequently see an overwhelming amount of answers, making very hard to choose the best actionable course.
Some of the answers frequently question the following parameters:
Light
In my experience corals can strive on different PAR unless the change was abrupt. If the light is the problem, corals in different depths will be affected differently.
Flow
I have seen tanks striving with very different flow conditions. The problems I have seen is the presence of too much focal flow in one coral, killing the side of the coral that was being blasted. Not enough flow will usually cause detritus to build up and lead to cyano or algae problems.
NO3 and PO4
We have seen many cases of thriving reefs with very low NO3 and PO4, as well as very high levels. Tests results of zero NO3 or PO4 does not mean that the corals are starving. I have tanks with healthy growth and color that frequently had zero NO3 and PO4. To kill a coral by starving it, in my opinion, will take months if you have fish in your tank and feed them frequently.
pH
I have had situations where my pH was lower than 7.9 with no change to polyp extension. Tanks using Ca reactors will often run on lower pHs and there are many examples of beautiful SPS reefs on that situation.
Temperature
Corals can increase their ability to deal with temperature spikes. A tank with a constant temperature with very little change would have more trouble with a temperature spike than one that has 2 or 3 degrees variation daily.
Alkalinity
High alkalinity in a low nutrient system is know to cause tip necrosis. If that is not the case and the alkalinity is between 6.4 and 11 I would not do anything about alkalinity. Changing the alkalinity would only add to the stress. My systems run at 6.4 to 7.5 withouth any problem. Many other systems have 8 - 11 and are sucessful.
Also, we frequently see many posts suggesting water changes. Sometimes, even large (i.e. 30% or more) volumes. Here is something that I believe can be more detrimental than help. Even though corals can deal with changes in parameters (e.g. when we add a frag to a new system), an already stressed coral may respond differently. Also, larger colonies tend to be less forgiving than frags. In my systems, I have continuous water change of about 1% per day. I believe stressed corals will usually benefit from stability.
Another aspect of troubleshooting is how you measure if the changes you are making are helping the situation. In my experience, stressed corals may take a long time (weeks to months) to respond to changes. A good strategy is to add a new, healthy frag to the system after the corrections were made and see how it respond. I belive some people keep changing things because they are looking for more imediate response from the stressed corals.
If the corals are not doing well in one of my systems and I don't know the reason I usually will add a good activated carbon (I like ROX 0.8) in a reactor with low flow, about 1 x the system volume per day. I may also increase the water change to 20% per week. Note that my water change is very slow (is 20% under the course of a week) and would likely not cause a lot extra stress to the corals. For systems with stressed corals I would not do more than 10% water change per day. I probably would also order a Triton test.
If any problem was evident in the Triton test I would address it. If no problem was obvious, I would wait about 3 to 4 weeks keeping the system parameters as stable as possible before testing if the problem was corrected with a new healthy frag. That is usually enough time for changing a significant amount of water from the system and allow for an equilibrium.
It is my impression that one of the most common cause of problems is making frequent changes chasing an improvement in the stressed corals without giving enough time or without using a new coral to test the effectiveness of the changes.
If you can identify a parasite or other types of pests, treatments for those are debated in many great threads. The discussion in this post is more directed to the situations where the cause of the problem is unknown. We see many people asking for help to troubleshoot systems that are not thriving, and we frequently see an overwhelming amount of answers, making very hard to choose the best actionable course.
Some of the answers frequently question the following parameters:
Light
In my experience corals can strive on different PAR unless the change was abrupt. If the light is the problem, corals in different depths will be affected differently.
Flow
I have seen tanks striving with very different flow conditions. The problems I have seen is the presence of too much focal flow in one coral, killing the side of the coral that was being blasted. Not enough flow will usually cause detritus to build up and lead to cyano or algae problems.
NO3 and PO4
We have seen many cases of thriving reefs with very low NO3 and PO4, as well as very high levels. Tests results of zero NO3 or PO4 does not mean that the corals are starving. I have tanks with healthy growth and color that frequently had zero NO3 and PO4. To kill a coral by starving it, in my opinion, will take months if you have fish in your tank and feed them frequently.
pH
I have had situations where my pH was lower than 7.9 with no change to polyp extension. Tanks using Ca reactors will often run on lower pHs and there are many examples of beautiful SPS reefs on that situation.
Temperature
Corals can increase their ability to deal with temperature spikes. A tank with a constant temperature with very little change would have more trouble with a temperature spike than one that has 2 or 3 degrees variation daily.
Alkalinity
High alkalinity in a low nutrient system is know to cause tip necrosis. If that is not the case and the alkalinity is between 6.4 and 11 I would not do anything about alkalinity. Changing the alkalinity would only add to the stress. My systems run at 6.4 to 7.5 withouth any problem. Many other systems have 8 - 11 and are sucessful.
Also, we frequently see many posts suggesting water changes. Sometimes, even large (i.e. 30% or more) volumes. Here is something that I believe can be more detrimental than help. Even though corals can deal with changes in parameters (e.g. when we add a frag to a new system), an already stressed coral may respond differently. Also, larger colonies tend to be less forgiving than frags. In my systems, I have continuous water change of about 1% per day. I believe stressed corals will usually benefit from stability.
Another aspect of troubleshooting is how you measure if the changes you are making are helping the situation. In my experience, stressed corals may take a long time (weeks to months) to respond to changes. A good strategy is to add a new, healthy frag to the system after the corrections were made and see how it respond. I belive some people keep changing things because they are looking for more imediate response from the stressed corals.
If the corals are not doing well in one of my systems and I don't know the reason I usually will add a good activated carbon (I like ROX 0.8) in a reactor with low flow, about 1 x the system volume per day. I may also increase the water change to 20% per week. Note that my water change is very slow (is 20% under the course of a week) and would likely not cause a lot extra stress to the corals. For systems with stressed corals I would not do more than 10% water change per day. I probably would also order a Triton test.
If any problem was evident in the Triton test I would address it. If no problem was obvious, I would wait about 3 to 4 weeks keeping the system parameters as stable as possible before testing if the problem was corrected with a new healthy frag. That is usually enough time for changing a significant amount of water from the system and allow for an equilibrium.
It is my impression that one of the most common cause of problems is making frequent changes chasing an improvement in the stressed corals without giving enough time or without using a new coral to test the effectiveness of the changes.

