Top 5 Most Common Problems in a Reef Tank

Top 5 Most Common Problems in a Reef Tank

One of the more popular questions we receive is, “What are the most common problems in a reef tank?” Owning a reef tank certainly comes with it’s own set of challenges. As a hobbyist, you are bound to run into a number of issues with your reef tank. In this article, we will go over five of the most common reef tank problems, how to identify each issue and steps you can take to resolve them.

1. Algae

Pictured above: Algae

How to Identify:

The most common forms of algae found in a reef tank are: green hair algae, film algae (generally found on aquarium glass), green turf algae, bryopsis as well as green or red bubble algae.


High levels of both phosphate and nitrate, which are primary food sources for algae, will promote algae growth. When present at abnormally high levels, the algae will grow faster than your clean up crew can consume it.

How to Fix:

Tip #1: Manually remove as much of the algae as possible, then change 10-15% of the water every 3-5 days until nitrate and phosphate levels are within normal range. Water changes every 1-2 weeks can further help keep nitrate and phosphate low.

Tip #2: Adding a media reactor and running GFO (Granular Ferric Oxide), or other phosphate absorbers, are also effective for reducing phosphate. Running an additional reactor with bio-pellets can be an effective tool for reducing nitrates as well.

Tip #3: Maintain phosphate levels between 0.02 – 0.05 ppm and nitrate levels between 0.025 – 5 ppm. During an algae bloom, it is common for nitrate and phosphate levels to test at zero. However, that does not mean you don’t potentially have an issue. This is because a tank with an algae problem is consuming their nutrients as quickly as they become available. The bottom line? If you have algae, you have nutrients to feed it.

2. Cyanobacteria

Pictured above: Cyanobacteria

How to Identify:

Often mistaken as a type of algae, cyanobacteria is actually a type of bacteria (hence, the name). It is generally red, but it can also be green, brown or black in color. Cyanobacteria leaves a slimy, velvety and unsightly film upon sandbeds, rocks and coral. If left untreated, cyanobacteria can even smother and kill corals.


Cyanobacteria can be caused by high levels of phosphate, nitrate and other nutrients, generally in combination with poor water movement and/or poor or inefficient protein skimming. High nutrient levels can typically occur due to a lack of water changes, poor quality source water, overstocking and/or overfeeding.

How to Fix:

Cyanobacteria can often be difficult to eradicate, requiring both patience and persistence, but it can be accomplished!

Tip #1: Check the filters on your RO-DI unit to ensure they have not been exhausted and that your source water is good quality. The RO-DI unit maintenance is often forgotten, but changing filters on a regular basis is a crucial step to maintaining good water quality.

Tip #2: Remove as much of the cyanobacteria as possible using a siphon or turkey baster, then routinely change 10-15% of the tank’s water every 3-5 days thereafter.

Other tips to consider for preventing outbreak: Increase water flow, reduce the length of time that tank lights are turned on, avoid overfeeding and use a highly rated protein skimmer.

3. Dinoflagellates

Pictured above: Dinoflagellates

How to Identify:

There are many different types of dinoflagellates, but they are commonly identified by long, snotty-brown strands with air bubbles trapped inside, resembling tiny balloons. 


Unlike cyanobacteria that is caused by high nutrient levels, dinoflagellates (i.e. “dinos”) are most often caused by nutrient levels that are too low. As both nitrate and phosphate levels approach zero, this creates an environment where dinoflagellates are able to outcompete other organisms for resources. (Although they can be problematic at high levels, it is important to have a small amount of both nitrate and phosphate available in your tank for proper tank and coral health.)

How to Fix:

It generally requires weeks, sometimes even months, to fully get dinos under control. A consistent, daily routine for addressing this issue is key.

Tip #1: Manually remove as much of the dinoflagellates as possible using a siphon or turkey baster. Continue to manually remove as more appears.

Tip #2: Change out any filter socks on a daily basis as they will generally become clogged quickly by the dinoflagellates.

Tip #3: Gradually increase nutrient levels by dosing small amounts of both nitrate and phosphate, using ATI Nutrition or similar products, to bring the levels back up to within acceptable range. The presence of nitrates will make the bacteria inside of the dinoflagellates multiply until they explode and die.

Other tips to consider: Dosing a small amount of bacteria daily, such as Microbacter7, can help expedite the removal of dinoflagellates. When dosed, bacteria will outcompete the dinoflagellates for surface area. There is also some evidence they may even consume the dinoflagellates. Additionally, a UV sterilizer can sometimes help clear dinoflagellates. Dinos come off of rock and sand at night and float in the water column where they can be destroyed by the UV sterilizer.

4. Low Magnesium

Low Magnesium
Pictured above: Low Magnesium

How to Identify:

Low magnesium levels are most evident when it becomes impossible to stabilize calcium and alkalinity levels. You may be dosing calcium and alkalinity daily, trying to keep both within normal ranges, but one or both continuously drop too low.

Proper magnesium levels prevent precipitation of calcium carbonate, which is critical to maintaining the proper levels of calcium and alkalinity. If you notice a white cloud of precipitation while dosing, calcium carbonate is likely precipitating out of solution. If this occurs check your magnesium levels immediately.  Additional signs of low magnesium level include bleaching of coralline algae, bleaching of small polyp stony corals and tissue loss on large polyp stony corals.


A common cause of low magnesium is failing to use a salt specifically designed for reef tanks that contains the proper magnesium levels. A lack of regular water changes to replenish consumed magnesium will lead to low levels as well.

How to Fix:

Tip #1: Perform regular water changes with a salt designed for reef tanks.

Tip #2: It is also important to test magnesium every other week, then dose whenever needed to maintain levels between 1250-1350ppm.

Click here to read more about magnesium and other important water parameters

5. Pests

Coral Pests
Pictured above: Coral Pests

How to Identify:

Pests are noticeable when you have retracted polyps, browning of coral, tissue loss, bite marks or even coral death.  Most pests are extremely tiny or camouflaged to coral tissue making them impossible to see.  The most common coral pests are flatworms, such as red planaria and acro-eating flatworms. Coral-eating nudibranch and red bugs are also common among smooth-skinned, small polyp stony corals.


Not dipping or quarantining corals before adding them to your display tank can bring unwanted intruders along with them.

How to Fix:

At a bare minimum, it is important to dip all corals before adding them to any reef tank. Also we recommend purchasing corals from a supplier that quarantines for at least 1 month prior to sale. If they do not, we recommend self quarantining for 1-2 months before adding any coral to your display tank.

Preventing any pests from entering into your reef tank is the best option as adding corals with pests puts all other corals at risk. The most effective treatments are not safe for reefs, so corals need to be removed for proper treatment. Of course, removing corals already encrusted onto the rocks is problematic.

Prevention is the absolute best way to keep your reef tank healthy and thriving! Weekly maintenance and testing can help prevent many common reef tank issues.  Additionally quarantining all corals and treating them with coral dip prior to adding them to your display tank can prevent possible outbreaks of pests. Otherwise, you might risk destroying your entire collection of corals!

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