Dinoflagellates are microscopic single celled organisms that are photosynthetic. They are very widespread in nature. There are over 2,000 different types of Dinoflagellates that can be found in different marine and fresh water environments. This is the basis of why Dinoflagellates can be such a problem to get rid of in a marine aquarium. To make matters much more challenging, Dinoflagellates can look a lot like cyanobacteria as well as other types of algaes if you do not have firsthand experience with them.
Appearance:
One of the descriptions that I have read and remembered the best is that Dinoflagellates looks like runny brown boogers with air bubbles. While funny, that is somewhat accurate. The most common color for dinoflagellates is a shade of brown, but they are also common found in a pale brown to off white / yellow color as well as a few different shades of green. The will start to coat object inside your aquariums as well as / or coating the aquarium glass. This coating will look like slime and be one of the above mention colors. It is also common to see gas bubble trapped by it and even a stingy appearance as the gas bubbles try to escape.
Dinoflagellates are a problem to have in your aquarium for two main reasons:
A) The vast majority of commonly found Dinoflagellates in marine aquariums are toxic to most forums organisms that you will keep in a marine aquarium
B) The can cover/coat corals to the point of stress them and even killing them
Actions to take to deal with Dinoflagellates
Dealing with Dinoflagellates has driven hobbyist to break-down their aquarium and start from scratch again or even leave the hobby. In the vast majority of these situations, not quickly reacting to the problem or using a incorrect method to deal with the situation resulted in either no changes or very limited success. Quick recognition and actions taken to get rid of them are critical.
As there are over 2,000 different types of Dinoflagellates, knowing which course of action to take can be a little difficult as one method that would quickly kill-off one species of Dinoflagellates will not slightly affect another. This is also why the internet has many stories of one approach working perfectly in one person’s aquarium while not in another aquarium which results in many people arguing for or against certain approaches. It is always best to take a combination of methods at once to help ensure success in a shorter period of time. Based on my experience getting rid of this stuff, I would suggest taking a the below describe approaches:
1) Reduce available nutrients in the water
2) Add additional granular activated carbon to your set-up (catalytic activated carbon is the best)
3) Black-out all lighting for a period of 24 to 72 hours followed by a reduction in the photo period
4) Reduce feedings to every second day
5) Manually remove as much of the Dinoflagellates as possible every day
6) Set you skimmer to over skim requiring the cup to be emptied at least twice daily
7) Use a 200 micron filter sock.
The above actions have worked for me on two different occasions in two different. If you do see progress after 4 to 5 weeks with the above steps, there are a few other things you can try.
1) While maintaining the above sets, stop completing water changes
2) Increase your magnesium levels to 1400 ppm to 1600ppm
3) Increase and maintain the pH to 8.3 to 8.5
4) Add a refugium or algae scrubber
5) Start bacteria dosing
6) Change brands of salt and start using RO/DI water if you are not already
1) Reduce available nutrients in the water
Reducing the nitrates to 2ppm or less and keeping the phosphate levels to undetectable levels will help kill off the Dinoflagellates. Using a good phosphate remover and carbon dosing are the two of the most common approaches to achieve this. The theory behind the nutrient reduction is that when dinoflagellates are in a very low nutrient environment, the bacteria inside their bodies will reproduce to the point where they will die off. This is one time that you cannot trust your test kits while you have a lot of dinoflagellates in your aquarium as they will consume nitrates and phosphates almost instantly. You have get assume the levels are high, take steps to reduce them, and start testing once they are on their way out. The following thread explains carbon dosing:
http://www.reefaquarium.com/2012/carbon-dosing-in-laymans-terms/
2) Add additional granular activated carbon to your set-up (catalytic activated carbon is the best)
The reason for this is that most of the dinoflagellates found in aquariums is also toxic to fish and inverts. This is why you can commonly find dead snails in a aquarium with dinoflagellates, they try to eat it and end up ingesting the toxins which kills them.
3) Black-out all lighting for a period of 24 to 72 hours followed by a reduction in the photo period. As Dinoflagellates are photosynthetic, this will cause a large scale die-off, and when followed by a reduced lighting period, it will go a very long way to help prevent thier return.
4) Reduce feedings to every second day
This will allow you to remove nutrients from the water even before they are added. Feeding every second day for extended periods of time will not harm or effect the health of your fish
5) Manually remove as much of the Dinoflagellates as possible every day. Siphon these little devils out of your tank each day. Clean up everything you can so you will not allowing them to reproduce and spread even further in your aquarium
6) Set you skimmer to over skim requiring the cup to be emptied at least twice daily the dinoflagellates for nutrients. In addition, it will help to keep your carbon dioxide levels low. Just remember with each skimmer cup you empty, replace the same water volume in the aquarium with freshly made salt water.
7) Use a 200 micron filter sock in your set-up.
This can help filter out any free floating dinoflagellates from the water that your skimmer may not remove
Other options to try when the above actions do not help after about 4 to 5 weeks of trying.
1) While maintaining the above mentions steps, stop completing water changes.
As dinoflagellates will use trace elements from the water, the theory is that stopping water changes, you can eventually starve them out. Through the replacement water from the manually cleaning and empting the skimmer cup, you will be replacing some of the water though. This would be one of the last things that I would recommend trying
2) Increase your Magnesium level to 1400ppm to 1600ppm.
This has shown to be effective in a few different types of dinoflagellates.
3) Increase and maintain the pH to 8.3 to 8.5. Maintaining a higher pH can cause some types of dinoflagellates to die off. The following link explains it a lot better that I can. This would be one of the last things that I would recommend trying as well. If not done correctly, you can cause damage/stress to corals and fish. The following thread will explain this a lot better than I can:
http://www.reefkeeping.com/issues/2006-11/rhf/
4) Add a refugium or algae scrubber
These both will help to remove nitrates, phosphates and a few other certain trace elements that some dinoflagellates will need to survive. Please note, you cannot alter your pH or Mag levels if you are trying to use a algae scrubber or refugium
5) Start bacteria dosing
Sometimes the common sold bacteria can out compete dinoflagellates for certain resources in the water.
6) Change brands of salt
Dinoflagellates do need certain trace elements from the water. If you were to change your bands of salt, you could be removing these trace elements causing the dinoflagellates to die off. Starting to use RO/DI water with 0 TDS (Total Dissolved Solids) will also help if you are currently using tape water.
Preventing Dinoflagellates
The best advice that I can give you is to have a properly planned tank and to have your water parameters in line at all times.
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and has no ill effects on the coral as you know. 
