Cloudy Aquarium – Diagnosis & Fixing Guide

Have you just walked downstairs or into the room and your aquarium water is cloudy? Have you begun to panic a little? Well, don’t. Diagnosis is the key to a cloudy aquarium and we need to know the cause before we can treat.

A cloudy aquarium is usually caused by sudden algae blooms, a coral spawning event, bacterial blooms, microbubbles from a pump or powerhead or from high flow stirring up the sandbed. Diagnosis is the key to determing if its a mechanical, biological or a chemical issue which can then be addressed.

Many of the causes of a cloudy aquarium are pretty easy to diagnose so lets go and see what caused your heart to skip a beat!

How Do You Diagnose Reef Tank Water Cloudiness?

You want to begin with eliminating the obvious.

Determine if its bubbles or sand:

  • Has your powerhead fallen off its mount, has the suction cup let go and it’s now blowing all the sand around the tank?
  • Did you purchase a Sand Sifting Goby the day before? Their name says it all.
  • Has the powerhead been knocked and is sucking in air from the surface and creating mass bubble chaos?
  • Has your protein skimmer developed a problem and firing bubbles out of the pump and into the sump?
  • Has your water level dropped and the return nozzle is now pulling in air from the surface and creating bubbles?

These are usually simple to fix if its a mechanical issue. If its the Sand Sifting Goby, you may want to vacuum the sand bed to remove the majority of the fine particulate matter that has settled within the bed.

Did you have any Anemones?

Did you own an Anemone that has unstuck itself and been dragged into a powerhead – Large emergency water change & run Activated Carbon if this is the case!

If the anemone has been mashed up and it has likely ejected toxins into the water. You need to be swift to get the toxins out before they begin to affect the other fish and corals.

Anemone Guards Are Great Protection

Run activated carbon is mesh bags , turn on the UV if installed and do several large water changes over the next few days and cross your fingers.

To help prevent future situations many pumps and powerheads can be fitted with cages and foam protection devices to prevent active amenones being pulled in and minced up.

What Color is the Water? Green or Milky?

Green = Algae-based problem
Milky  = Bacteria, Coral Spawning or Precipitation based problem

More on these causes later…

Did Your Aquarium Go Cloudy During Its Cycle?

Cloudy water during an aquariums initial cycle may be due to insufficient nitrifying bacteria to convert the bio waste currently in the tank. Too many fish may have been added too soon after or even during the initial cycle. Water changes and adding a live bacteria culture can help clear the water.

During your aquariums cycle, you are allowing time for aquariums beneficial nitirfying bacteria to build in your system to deal with the Ammonia, Nitrites, and Nitrates that your livestock releases each time they go to the bathroom.

When there are not enough bacteria to manage the waste you could see the water have a cloudiness or haze to it as the Bacteria blooms. These can last from several days to several weeks depending on your situation. As time passes, the water will clear as the beneficial bacteria multiply and deal with the issues causing the cloudy water. As you have probably heard many times already, Be Patient!

Did Your Aquarium Water Go Cloudy After A Water Change?

When mixing saltwater for a water change, elements from within the salt mixture can come out of suspension and remain floating. When adding this water to the aquarium it can appear to make the water cloudy. With time the mechanical filter stage should capture the particulate matter ready for removal.

Mixing saltwater can sometimes give you headaches! It is rare but sometimes you can have a new batch of salt that takes longer to fully dissolve into the water. I usually begin mixing my new saltwater batch a day or two before I do my water change to ensure thorough mixing, but you may not have that situation available.

If your water is cloudy after a water change these are probably the most common reasons:

  • Salt not fully dissolved – Patience, it will dissolve with time
  • If you have disturbed the sandbed during vacuuming or adding the water this will have released dust and detritus into the water column. Allow your filter floss or filter socks to remove the suspended particles
  • Microbubbles are always present for a few hours after a water change. The mixing of the water, adding the water and general messing around with the water all adds microbubbles. Again, patience will see them clear

For More Information on Water Changes Check Out this Article:

Saltwater Aquarium Water Change – Your First Time

Did Your Saltwater Aquarium Go Cloudy Overnight?

It is not uncommon for corals in an established aquarium to spawn during the night. Large sperm and eggs masses can be released into the water causing the water to appear milky when the lights turn on in the morning. Mechanical filtration and a water change are the easiet ways to remedy this.

Do you have a tank full of thriving corals and you woke up to a cloudy tank? It’s not uncommon for corals to spawn during the night once they are happy and thriving, especially if you have multiple corals of the same species.

Depending on how many spawned will depend on how cloudy your water became. Your corals may have been spawning for years but only on a small scale and your filtration removed any trace of it before your lights came back on the next day.

Coral Spawning

This year may be different! You could have had a mass spawning event and it’s taking a while for your filtration to clear it. Run through the items in this article to ensure it is not something else causing the cloudiness and if not, congratulations! You could have a thriving Reef! To me, having an animal reproducing in your aquarium shows it is happy and all its needs are met!

On the other hand, if you have no corals in your aquarium, or you only have a few and they are new, then spawning is not likely to be the cause.

How Do You Get Rid Of Milky Water In A Fish Tank?

Your aquarium is full of different types of bacteria all doing a specific job, you have Nitrosomonas Bacteria that convert Ammonia into Nitrite, you have Nitrobacter Bacteria that converts Nitrite to Nitrate and you have Bacteria that feed off organic waste such as uneaten food, poop, and detritus, just to name a few.

The bacteria that most likely caused a milky cloudiness to your aquarium are called Heterotrophic Bacteria and these are the ones feeding on the decaying waste. They can have explosions of multiplication when a food source is in abundance. A water change and reguar maintenance will remedy this.

What this shows you is that you need to do more to remove the decaying matter in your tank. More frequent water changes, vacuuming the sand bed, turkey basting your rocks, cleaning your floss/socks more often, increasing your clean-up-crew or reducing your bio-load by having less fish or feeding less. The cloudiness will soon clear with a bit of maintenance and a water change!

Bacterial blooms are nothing to get panicked over, its just mother nature taking advantage of the abundance of available food. As time goes on, the different bacteria will multiply to help deal with the bio-load and hopefully, your increased maintenance will prevent this from happening in the future.

If you find this is happening regularly and your maintenance is good then you could look at adding a UV Sterilizer to your system. They come in all sizes to accommodate every tank size and the sterilizer will kill any bacteria that flows through it. This could help control the cloudiness if you have tried everything else.

If I was going to install a UV system on my aquarium I would definitely look at the great range of sterilizers from Aqua Ultraviolet here at They come in a vast range of sizes to accommodate any system and are bacteria sterilizing machines!

Aqua UV Sterilizer
Aqua UV Sterilizer

I know of a few owners who love them and they really helped clear their water.

For even more information on UV Sterilizers, you can read my article –
Aquarium UV Sterilizers – What Do They Really Do?

How Do You Get Rid Of Green Water In Your Fish Tank?

Suspended algae matter is the most common cause of green aquarium water. An abundance of food has caused a growth explosion. Water changes with high-quality water, regular maintenance, installing a refugium or turf scrubber, or running Bio-pellets all help reduce the food source algae thrives on.

If they multiply enough there can be cases where you cannot even see the fish! I have seen this many times on freshwater aquariums where the maintenance has been poor at the best of times!

The excess algae bloom is usually fuelled by one or more of the following situations:-

Too Much Light

Algae is a plant and it uses photosynthesis to convert light to food. If your aquarium has too long a lighting period or has direct sunlight you will get more algae growth. I have one small corner that receives direct sunlight first thing in the morning and that corner is always greener than the rest of the glass.

If this may be a cause, shade the tank somehow from the direct sun or reduce the lighting period on your lights. I like my lights on more in the evening when my family and I are around so my lights ramp up from noon and then ramp down beginning at 10pm. I have good algae growth on my glass but I Mag-Scrape (Magnetic Glass Cleaner) my glass every 2 days.

Excess Nutrients

Do you have a lot of fish? Do you overfeed? We all do at some point! Excess nutrients are just fuel for algae. Algae love Nitrate, Phosphate, and light to thrive and a good way to provide the first two is a heavy bio-load. Having a lot of fish and feeding them regularly is OK providing you clean up!

Make sure to vacuum your sand bed and turkey baste your rock before a water change are great ways to help remove detritus. Same goes for the sump, turkey baste any sitting waste and get it into the water column. The more waste you have sitting, the more it will break down into Nitrate and release Phosphate into your water, fuelling the algae.

High Levels of Phosphate

As just mentioned, algae loves Phosphate. The higher the level you have, the more food you are providing for the algae. Get the detritus removed to prevent it from releasing the Phosphate into the water.

High Levels of Nitrate

Just as Phosphate, the higher level you have, the more food you are providing for the algae. Regular water changes are a great way to help keep Nitrate low.

To also help, you can also view my article on lowering Nitrate HERE

Tips To Help Make Your Saltwater Aquarium Crystal Clear

  • Regular water changes
  • Don’t overfeed
  • Install a Refugium ==> See my article HERE on Refugium’s <==
  • Vacuum sand bed and turkey baste rocks & sump weekly
  • Mag-Scrape your glass often
  • Keep filter floss and socks clean
  • Keep your Protein Skimmer clean and working efficiently
  • Have good water surface agitation for gas exchange and keep oxygen level high
  • Keep powerheads from disturbing the sandbed
  • Have a Bubble Trap in the sump after your Protein Skimmer
  • Use good quality Activated Carbon. Change it regularly
  • A UV sterilizer is another solution since UV light will kill microorganisms in the water such as bacteria, algae, and viruses. In theory, good guy micro-organisms in the rock and sand are not killed since they must be free-floating and pass through the UV sterilizer.

To Finish

Just like many of the other methods of controlling a parameter or issue within your saltwater aquarium, it requires a multi-angled approach. By having a good, regular maintenance schedule and incorporating some of the tips listed in the article your phase of cloudy water will be short-lived and hopefully not to be seen again (Unless its coral spawning which is a good thing!).

Many of the problems I see with beginners are mainly caused by either their first time experiencing the issue or the lack of knowledge on what caused the issue.

Further Reading

If you found this article helpful, may I suggest a few more for you:


Hi, I'm Richard and I have been an avid aquarist for over 30 years with a passion for Saltwater Aquariums. I love to pass on my knowledge to help others get the same amount a pleasure out of this hobby as I do. View my About Me page to find out more about me & my mixed reef aquarium.

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