Setting Up and Cycling a Saltwater Aquarium for Seahorses and Fish



What does Cycling an Aquarium Mean?

"Cycling an aquarium" means you are allowing for enough nitrifying bacteria to populate the biological filter to metabolize the toxic ammonia fish create via waste.There are many ways to properly cycle an aquarium. This process can take up to 4-6+ weeks, patience is key with saltwater aquarium keeping.

To simplify, fish create waste which adds ammonia (NH3) to the aquarium. Beneficial nitrifying bacteria when present quickly metabolize this very toxic ammonia into nitrite (NO2, also very toxic to fish) and then to Nitrate (NO3). If you do not have enough beneficial bacteria in the aquarium you will get an ammonia and/or nitrite spike which can quickly lead to death and other problems with your fish and live stock. Making sure your aquarium is well established and fully cycled is extremely important to prevent losses. We will be covering how to accomplish this and properly setup your aquarium in this article.

What Size Aquarium and Filtration?

Aquarium Size

There is a huge variety of aquarium fish available so if you are planning your saltwater aquarium you want to familiarize yourself with what fish species are available, what you would like to keep and their tank size requirements.

Aquariums for Seahorse

For our large seahorse species (not Dwarf seahorses, H. zosterae) we recommend a 30 gallon minimum aquarium size for the first pair and an additional ~15 gallons for every additional pair you wish to keep. If possible, going larger is even better and gives you some wiggle room as well as room to expand your herd later which most hobbyist end up wanting to do. Your seahorses will enjoy the space and many of our larger seahorse species reach 5-7+ inches with maturity, they grow to be large fish.

While 30 gallons is the minimum aquarium size we recommend for keeping seahorses, an aquarium in 45-90+ gallon range will allow you to keep a much larger variety, give your seahorses as well as other animals more space, and you likely will not have to worry about upgrading to a large tank size later.

There are many all in one (AIO) aquariums on the markets now days. These AIO aquariums often include a back compartment that houses the return pump, media, heater and other equipment. Another option is having a sump which is basically a second aquarium under your display aquarium to house equipment and filteration so this is out of view. Having a sump gives one a lot more options and flexibility with filtration. The extra water volume with a sump helps stabilize the aquarium. Canister filters can be used for saltwater aquariums but they can be a bit time consuming to take apart and do maintenance on. If not properly maintained, canister filters can be nutrient and potentially harmful bacteria sinks in a seahorse and any saltwater aquarium. A standard hang on the back filter by itself is not going to be enough filtration for a seahorse aquarium. In our experience, the best option when possible is having an aquarium with a sump.


Water Flow/pump

Having enough and proper water flow is one of the most important factors in setting up a healthy environment for your animals. Every aquarium is going to be unique and a bit different. We recommend aiming for 10 to 25 times turnover with your saltwater aquarium for seahorses and most other fish. So if you have a 30 gallon aquarium you should be moving around 300+ gallons of water per hour. This can be achieved via return pumps and additional powerheads may be necessary. You do not want to have dead spots that allow for waste to settle. Having some lower to moderate flow ares for your seahorses to rest is recommended but overall you do not want to have low flow in your aquarium! Flow is very important as it allows for the filtration to filter the water properly, gas exchange and more. Too little water flow will lead to poor gas exchange which will lead to a build up carbon dioxide and low pH. Oxygen levels can quickly deplete as well. Too little flow will allow with undesirable waste and detritus to accumulate in the aquarium leading to an unhealthy and unstable environment for your animals. 

Protein Skimmer

We highly recommend using an over sized protein skimmer with seahorses and any saltwater aquarium. Small nano tanks under approximately 10 gallons can usually get away without a protein skimmer as large water changes are easy and these small tanks are going to have a small bio-load. Using a protein skimmer will greatly reduce organic build up in an aquarium. Protein skimmers help reduce undesirable nutrients in the aquarium by pulling out waste before it breaks down further. Besides a limited stocked small nano tank, we would not setup a seahorse or saltwater aquarium without a skimmer. Seahorses are messy fish and for them we recommend ideally going with a skimmer that is twice rated for your aquarium. For example, if you have a 30 gallon aquarium we recommend using a protein skimmer that is rated for at least a 60 gallon aquarium. A protein skimmer will also help prevent a build up of inorganics in your system as well.  

SCA Protein Skimmer, one we highly recommend for those who are using a sump 

Live Rock, Substrate, Media or a Combination of Both

What is liverock? Natural Live Rock

Live rock is a term used to describe calcium carbonate based rocks from the ocean that have living micro-organisms often including nitrifying beneficial bacteria, desirable purple coralline algae, copepods and more. It can have other living organisms and sometimes unwanted "hitch hikers" that can be harmful to the aquarium so one wants to be cautious and observant when using these in the aquarium. Liverock has the beneficial nitrifying bacteria the aquarium needs to metabolize ammonia to nitrites to nitrates. It is also important to buffer and maintain pH in the saltwater aquarium. In general, we recommend about a pound per gallon give or take in the aquarium.

When using natural liverock from the ocean one needs to be aware of how it has been handled. If the liverock has been dried out, some or all of the live organisms on it may have died off. If this is the case, this will add toxic ammonia and likely cause some bacterial blooms so one will need to wait for the nitrifying bacteria to metabolize this and the breakdown of these organisms to complete. You want to make sure you have no ammonia or nitrites for at least a week before you try adding fish.

Using natural live rock can create a very realistic reef display and add a lot of diversity to your home aquarium.

Manufactured Liverock

Now days there is some really nice manufactured, man-made, liverock available. This is what a lot of hobbyist are using now days to avoid pest and unwanted hitch hikers. Real Reef liverock is our favorite manufacturer of liverock for saltwater aquariums. This rock is seeded with nitrifying bacteria. It also has safe dyes as well as live coralline algae to make it look very realistic and natural. 

If starting with all liverock and live sand you likely will not see much of a cycle at all with your aquarium meaning you likely will not see any detectable ammonia and nitrites. We recommend keeping a very close eye on your water parameters including ammonia, nitrites, and nitrates. It is also important to stock the aquarium slowly and not add too much at one time. This way your beneficial nitrifying bacteria populations have time to populate. 

Photo credit Real Reef Manufacturing, Inc

Dry Rock

Dryrock is calcium cabonate based rock from the ocean that has been completely dried out. There is also fossilized coral reefs that are mined for dry rock for aquariums. This rock has no living beneficial bacteria or micro organisms. It is often a lot less costly than liverock which is a benefit. Being dried out, you are not going to have undesirable hitch-hikers but the cycling process will likely take longer.

Since dry rock has no living beneficial nitrifying bacteria you will want to seed the aquarium with nitrifying bacteria after adding this rock. We recommend using FritzZyme 9 or Dr. Tim's One and Only nitrifying bacteria products for seeding the aquarium when starting with all dry rock. Nothing will be breaking down in the aquarium to allow these bacteria to populate so it is helpful and often necessary to add Ammonium choride (ammonia) to allow the beneficial bacterial to populate and make sure your aquarium can handle your future fish bio-load. We recommend Dr. Tim's Ammonium chloride product and follow the manufacture's instruction for dosage. By adding Ammonium chloride to your uncycled aquarium you are essentially "feeding" these beneficial bacterial populations while they establish in the aquarium. It is VERY important to remember this process is adding straight ammonia to the system which very toxic to fish and other living organisms. You do not want to do this if your aquarium has live fish and invertebrates in it! It will kill them! This method of "ghost" dosing the aquarium will allow the aquarium to cycle. Testing the water daily during this cycling process is helpful to know where the aquarium is at in its cycle. You will see detectable ammonia at first. Once enough bacteria build up to metabolize the ammonia (NH3) it will convert to nitrites (NO2) and then eventually to Nitrates (NO3). Ammonia and Nitrites are very toxic to fish and invertebrates (crabs, snails, corals, ect). Nitrates under <25 ppm or less are ideal. Often times when "ghost" dosing ammonia you will end up with very high nitrates so a large water change(s) may be necessary to bring these down after you have completed the cycle and before adding fish.

This method of adding Ammonium chloride for cycling a new aquarium is a much cleaner method than some other methods we have heard of. Some hobbyist will add frozen or pellet food to the aquarium and allow this to rot in the aquarium to create ammonia. When doing this you are allowing potentially nasty bacteria to also build up in the aquarium which is not good. 

Photo credit, Tevin Lee in Singapore

Substrate-Sand or Bare Bottom (no Sand)

Some hobbyist prefer to have a natural looking sand bed in their aquarium and others prefer no sand also refereed to as a bare-bottom aquarium. We will be covering both options.


Having sand in the aquarium is more aesthetically pleasing to most keepers. A sand-bed in the aquarium creates a more natural look. You can also have a variety of sand dwelling clean up crew inverts including Nassarius snails, Cerith snails and sea cucumbers which really need a sandbed to thrive. Nassarius snails are especially good clean up crew with seahorses as they help eat leftover meaty foods. You will also have a lot more beneficial micro-fauna with a sand-bed.

If you are interested in keeping other tank-mates with your seahorses this may also play into your decision on whether to go bare bottom or with sand. Some species of gobies are substrate dwelling and really do best with a sand-bed. In addition, there are a variety of beautiful rooted macro-algaes that can be kept with seahorses too. It is important to really research and understand the needs of the animals you wish to keep.

If you decide to go with sand in your seahorse aquarium we recommend using an aragonite substrate in the ~0.5-1.5 mm range. CaribSea Fiji Pink aragonite is our favorite. Avoid larger substrate such as crushed coral. Over time larger substrate will allow for a build up of detritus and waste. We have seen a lot of hobbyist have issues keeping their seahorses in an aquarium with coarse crushed coral substrate.

Using live sand meaning sand with living nitrifying bacteria can also really help speed up your aquarium cycling process.

Having sufficient water flow near your sand-bed will also help prevent build up of waste and keep the aquarium healthier.

Photo credit Savannah Coon

Bare Bottom (no Sand)

Having a bare bottom aquarium (no sand) can make keeping your aquarium cleaner much easier. With no substrate on the bottom it is easy to make sure waste isn't building up in the aquarium. Build up of detritus (waste) in the aquarium creates instability and can promote nasty bacterial growth that can make your seahorses more susceptible to problems. Keeping build up of waste out of the aquarium is one of the keys to long term success with seahorse and saltwater aquarium keeping. If your aquarium is bare-bottom and you are getting a build up of food or waste on the bottom you need to add more water flow or tweak the water flow at the bottom of the aquarium.

From our experience, we find it much easier to keep the aquarium clean and water quality up with having no sand.


MarinePure Media 

In addition to liverock, we really like using MarinePure media in our systems. This is a highly porous ceramic based product that has a ton of surface area for nitrifying bacteria to populate. We use this media in our sumps but it can also be added directly to the display tank, in hang on the back filters, or canister filters. This will drastically increase your beneficial bacteria population with time and allow for much higher stability in the aquarium. We highly recommend using this. 

Sump at our farm with MarinePure media blocks, SCA protein skimmer, filter socks, UV sterilizers, Carbon, heater and return pump

Nitrifying Bacteria-Good Bacteria in the Aquarium

As we mentioned before, Fritz Aquatics FritzZyme 9 Saltwater Nitrifying Bacteria is one of our favorite products for adding to the aquarium when you first set it up. This will give you a boost of beneficial nitrifying bacteria to help ensure you have enough "good" bacteria in the aquarium. This can be used and is also beneficial in any new aquarium, not just one started with dry rock. Dr. Timm's One and Only Live Nitrifying Bacteria is another good product for seeding your bio-filters and aquarium with beneficial bacteria. Both of these products are commonly available at local aquarium stores and online retailers.

Photo credit Savannah Coon

Test Kits and Supplies

What Water Parameters Should You Test? 

Some of the basic water parameters one should test for in a saltwater aquarium include ammonia, nitrites, nitrates, phosphates, calcium, pH, alkalinity, specific gravity, magnesium and temperature. See chart below for recommended levels for most seahorses, saltwater fish, corals, and inverts. Salifert makes really good test kits and we recommend them. Another aquarium test kit manufacturer is API and Hanna. 

For checking salinity (salt concentration) in the home aquarium we highly recommend a refractometer. These are actually pretty inexpensive now days and can be found at most local aquarium stores and online outlets. Hydrometers are also available but they are less accurate and not as user friendly.


General Water Parameters for Seahorses


Recommended level

Specific Gravity





8-12 Dkh

Ammonia (NH3)

Undetectable (Toxic to fish and corals)

Nitrite (NO2)

Undetectable (Toxic to fish and corals)

Nitrate (no3)

(Ideally undetectable) <25 PPM

Phosphate (PO4)

(Ideally undetectable) <0.2 PPM


350-450 ppm


1250-1350 ppm


70-74 F (21-23 C) for most Seahorse Species. We keep H. comes at a slightly higher range (75-76 F). If keeping fish only (no seahorses) we recommend 76-79 F. If you are keeping peaceful fish with seahorses most handle the cooler range no problem.



We always recommend having a heater on your aquarium. Many aquarium heaters are now available with a digital temperature reading which is helpful for monitoring temperature. Having a heater will help keep the aquarium stable and prevent it from getting too cold. 

When keeping seahorses it is important to place the heater in your sump, back of your AIO or have a heater guard. If a seahorse hitches to the heater it can burn them so you want to keep it out of reach!

Royal Gramma                                      Toadstool Leather Coral

When is the Aquarium Ready for Fish and Corals?

Once you have all your rock in the aquarium, sand if you are going with sand rather than bare-bottom, proper filtration and the tank is fully cycled you should be ready to add some livestock. We recommend waiting at least a week from seeing no ammonia or nitrites before adding any live animals.

It is common for new tanks to go through a bit of an algae phase in the beginning. This is a good time to start adding "clean up crew" invertebrates to the aquarium. Clean up crew can include snails such as Astrea, Nassarius, Cerith, and Turbo, crabs including blue leg hermits, red leg hermits, Emerald crabs, as well as Peppermint shrimp ect. These inverts will eat the algae, waste and also help build up your beneficial bacteria. If you do not have algae growing in the aquarium you can still add invertebrates but you may want to lightly feed them. After this, if all is well, you can try adding a hardy fish or if you are confident you can add your seahorses.

It is very important to keep a close eye on your ammonia and nitrite levels after adding fish. You do not want to have a spike in ammonia or nitrite in your new aquarium. Making sure you do not have left over food sitting in the aquarium is also key. If you want to also keep live corals, macro algae, ect you can start adding easy to keep corals at the same time or shortly after you add your first fish. It is important to make sure you have proper lighting for keeping corals. We really like LED lighting and there are many available aquarium LED lighting options on the market these days. Having them programmable is definitely recommended so you can properly set them for your aquarium.

Photo credit Savannah Coon

Seahorse Savvy Display Aquarium, Yellow Clown Goby on a Feather Duster decorator worm

What Happens if you Get an Ammonia or Nitrite Spike in Your Aquarium?

If you test your water and you have detectable Ammonia or Nitrites we recommend adding an ammonia blocker such as Prime or Amquel right away.  In addition to adding an Ammonia blocker, you also want to do a large ~30-50% water change and add additional nitrifying bacteria to stabilize the system.

A spike in ammonia and/or nitrites in an already cycled aquarium means something went really wrong or you may also not have enough nitrifying bacteria in your aquarium and the tank is "recycling". This usually only occurs when one stocks the aquarium too quickly (too many fish), over feeds, rinses media in freshwater (this will kill nitrifying bacteria), power outages, stirs up the sand bed too much or some other issue.

Be prepared to continue to monitor your levels and do more large water changes. A common misconception is a large water change will remove too much beneficial nitrifying bacteria. Nitrifying bacteria are benthic meaning they are in your sand, liverock and media. They are not in the water column so no worries about this removing beneficial bacteria. When doing a large water change it is important to make sure the specific gravity and temperature match the system so you do not "shock' the system and animals. Any time you have something go wrong in the aquarium a large water change and adding fresh activated carbon usually helps.


Photo credit Cheryl Taylor, H. comes (Tiger Tail seahorse)

Hitching Posts for Seahorses

When setting up a seahorse aquarium you want to make sure you have plenty of "hitching" posts for your seahorses to hold onto with their prehensile tail. These can include branching artificial corals for saltwater aquariums, anchored plastic chains, live Gorgonian corals, live soft corals such as leather corals, macro algae and more. 

Does the Aquarium Need an Established Copepod Population Before Adding Seahorses?

This is a common question we get asked. Copepods are very beneficial in any saltwater aquarium but you do not need a huge population in a seahorse aquarium. Our larger species of captive bred seahorses are completely weaned to frozen Mysis shrimp and usually do not recognize tiny copepods as a food source. Copepods are definitely not enough to sustain seahorses in their aquarium. Our seahorses need to be fed frozen Mysis shrimp 2-3 times daily.

Thank you very much for reading. We hope you find this helpful. Understanding water parameters and balance in the aquarium is one of the keys to success. We love helping hobbyist, especially new hobbyist. If you have any questions please reach out. We are happy to help and want you to be a successful keeper. Also see links to more resources below.

Contact Information:


Phone: 410-618-3604

Hours: Monday-Friday 11:00 a.m. to 5:00 p.m. EST     

Red Ball Sponge                                    Purple Filly Photosynthetic Gorgonian

Other Helpful Resources and Further Reads

Basic Aquarium Husbandry and Maintenance

Temperature Range for Keeping Seahorses in the Home Aquarium and Why

Water Flow in a Seahorse Aquarium

Substrate in a Seahorse Aquarium-Bare Bottom vs Sand

Choosing Your Seahorse Species and Stocking

Feeding Your Captive Bred Seahorses

Tank-Mates for Seahorses-Fish

Tank-Mates for Captive Bred Seahorses-Live Corals

Why Mixing Seahorse Species is Not Recommended