Note from the Editor:

Keeping your tank clean is important for a saltwater system. It's not just important for the livestock, but it's also important for your viewing pleasure. We want you to feel happy when you look at your tank, not dread because the tank is dirty.

What may feel overwhelming for the beginner is much more manageable when you break it up into smaller tasks. So, the author of this article, Robert Woods, has done just that.

Photos included here are from the Reef2Reef archives, ©2019, All Rights Reserved. However, I will not credit the persons who kindly furnished the photos so as not to draw attention to them publicly.


An aquarium that needs a little cleaning.

Cleaning your aquarium is one of the most important aspects of keeping fish. To care for a reef habitat, the most important aspect of keeping your reef happy and healthy is by looking after the water. Very basically--you look after the water, and the water looks after its inhabitants!

With that in mind, we’re going to take a look at four important aspects to keep your tank clean, including; removing algae, cleaning the substrate, cleaning live rock, incorporating a maintenance schedule and how to clean an empty tank.

Method One: Getting Rid of Algae

A bit of an algae overgrowth.


There are a number of different types of algae that you might have in your aquarium; blue-green algae, red slime algae and green hair algae are a few examples.

If you find yourself with an excess of algae, remove whatever you can by hand or using a siphon. Depending on the type of algae you’re dealing with, increase or decrease the intensity of the lighting, use a protein skimmer to remove excess nutrients and choose a good quality salt mix.

You could also consider adding herbivores who like eating algae, such as snails and sea urchin.

It’s important to remember that removing the algae shouldn’t become a long-term maintenance plan. If you have an excess of algae growing in your tank, there is a reason for it so you need to find the source to prevent the problem. A few factors which can influence algae growth include:

· Inappropriate lighting.

· Using a poor quality sea salt mix.

· Poor maintenance on the aquarium.

· Not enough water flow/circulation.

· Overfeeding.

It’s also important to remember than some algae growth is actually healthy and natural; it’s only when the growth spirals out of control that it becomes an issue.

Method Two: Cleaning Live Rock

Some live rock that needs cleaning.
r2r2012 pics 019.jpg

To clean the live rock in your tank, you can either use a turkey baster or a small powerhead. Live rock is home to a wealth of beneficial nitrifying bacteria so you want to go easy on them.

Use the turkey baster or powerhead to clean inside all the nooks and crannies in the rock. You’ll see all the debris coming out with each blast of water. This debris should be picked up in the filtration system.

You might also want to add a clean-up crew to your tank; they do a great job of getting into all the space you can’t reach, keeping them clean.

Method Three: Cleaning the Substrate

Substrate that looks like it needs cleaning in the refugium.

You should never clean all your substrate at once. A bed of good bacteria will have established itself on the substrate in your tank, and cleaning it all in one go can lead to new tank syndrome where you’ll see spikes in ammonia and nitrites again – not good at all for your fish. This section does not apply if you have a deep sand bed (DSB) which should not be disturbed.

Instead, clean small portions, every week. The method of cleaning will depend on the type of substrate you have.

Coarse Substrates/Crushed Coral – perform a light cleaning using a siphon.

Small/Finely Grained Sand – gently rake the substrate with your hand to raise the debris to the surface. This should then be free to be filtered out by the tanks filtration system.

Method Four: Keep the Water Crystal Clear

Cloudy water.

The best way to ensure you have crystal clear water is to implement a strict maintenance schedule. Here is an example of an ideal cleaning schedule for your marine tank.


· Top off any water which has been lost to evaporation.

· Inspect and feed all the fish.

· Check the water temperature and specific gravity.

· If you keep corals, add calcium and buffering agent if this is part of your routine.

· Empty and rinse the cup from the protein skimmer.


· Check that all the equipment is functioning properly.

· Test ammonia, nitrite, nitrate and phosphate levels.

· If you have a reef, check the calcium and alkalinity too.

· Clean the glass with an algae magnet.

· Clean a portion of the substrate.

Aquarium glass that needs a bit of cleaning.


· Carry out a partial water change (the more heavily stocked the tank is, the more frequently you should do this).

· Replace any disposable media filter or at least rinse media filters in saltwater.

· General clean of any equipment and exterior of tank.

Method Five: Cleaning an Empty Aquarium

The simplest way to clean an empty aquarium is through using a damp cloth and white distilled vinegar.

Remove any large bits of debris from the empty tank before you make a start and then use hot water and a cloth to wipe all the surfaces free from dust.

Make sure any cleaning equipment you use for your tank is new and only ever used for your tank. It’s important never to use cleaning products as they often leave a residue which can be really harmful to your fish. Likewise, never use any household clothes or rags which have previously been used with chemicals.

Once you’ve removed all the dust, you can spray vinegar onto all the surfaces and leave it to dissolve any more difficult to remove stains, or water lines. Then, using a clean damp cloth, wipe the vinegar off.


We encourage all our readers to join the Reef2Reef forum. It’s easy to register, free, and reefkeeping is much easier and more fun in a community of fellow aquarists. We pride ourselves on a warm and family-friendly forum where everyone is welcome. You will also find lots of contests and giveaways with our sponsors.


Author Profile: @Robert Woods

Robert Woods is an expert aquarist who has been keeping aquariums, both freshwater and saltwater for over 30 years. He created the website "FishkeepingWorld dot com" as a hub of information for aquarists of all types.

His goal is to make keeping aquariums accessible for everyone. He likes to write articles especially for beginners in order to break down tasks into manageable chunks.