Protein Skimmers

Protein skimmers are a unique type of filtration that can be hard to wrap your head around if you’ve only worked with freshwater tanks before. On top of that, they aren’t exactly the cheapest piece of equipment for a reef, so it’s easy to see why so many people ask if they’re really even needed. The first time you empty a nasty protein skimmer cup full of muck, you’ll appreciate what they do.

Best protein skimmer for a
Protein Skimmer Waste

The Basics

At the most basic level, a protein skimmer is a chamber where water and fine air bubbles interact before the water drains back into the tank or sump. This interaction allows certain things in the water that are attracted more to air than water to ‘grab’ the air bubbles and ride them as they make their way up the skimmer chamber and into the collection cup. There is a collection cup on top where the waste and other effluent (or skimmate) is collected for you to dispose of it.

Protein skimmers can be hang-on-back (HOB), but the in-sump versions are much better. They are larger which allows them to be much more effective.

Waste Removal

Their primary function is waste removal. Certain types of waste are attracted to air bubbles more than water, so the bubbles collect that waste and trap it in the collection cup.

One of the best things about a protein skimmer is that it actually removes the waste from the water column as opposed to almost all other types of filtration that simply collect it for you. This difference means that the waste in the collection cup is no longer breaking down and releasing nutrients into the system.


Another often overlooked function of protein skimmers is aeration. Even a modestly sized protein skimmer will provide all of the aeration a tank needs. In fact, they’re so effective at aeration that the CO2 in the air that’s brought into the skimmer can be enough to lower the pH in the tank. CO2 in water creates carbonic acid which lowers the pH. This is why some people will use a CO2 scrubber on the air intake to their skimmer. It will remove all the CO2 from the air going in which can have a significant impact on the pH. Be aware though, there are many other factors that affect pH (such as KH and even the lighting schedule on your refugium), so you usually want to work through those before you jump straight to a CO2 scrubber on the skimmer.

What Size Skimmer Should I Get?

Anything is better than nothing. The normal guidelines are something to the effect of getting a skimmer rated for the actual tank size for a fish-only tank, but going as much as 3x the actual tank size for a reef. Bulk Reef Supply takes the opposite approach and says when in doubt, go smaller, as explained in the video below.

Which Brand?

There are lots, and lots, and lots of skimmers out there. I remember walking through the MACNA expo and seeing so many different brands that I just started thinking “How can they all be any different from each other, they’re all skimmers.” Some have real features that are worth having, some have extra bells and whistles, and some are great and then on top of that, you get to pay even more for the brand name.

In my experience, Eshopps is a great balance of high-quality while still being affordable. They aren’t the cheapest, but you are getting something for every dollar you spend on them and they are far from the most expensive out there.

Reef Octopus is another great one with the right features and ease of use without being overly expensive.

What Type of Pump

This may seem simple enough, but the type of pump on the skimmer can have a big impact on how well it works. There are two main types of pumps, AC and DC controllable. As with powerheads and return pumps, the DC controllable pumps are worth the extra cost. They have a controller where you can set the exact flow you want making it even easier to very precisely adjust and tune your skimmer. Reef Octopus has some skimmers with DC controllable pumps and is another great brand with high quality for a not unreasonable price (although, it is a step up from Eshopps in price).

HOB vs. In-Sump

This really isn’t much of a decision, you either have a sump in which case you should get an in-sump skimmer or you don’t in which case your only option is a HOB skimmer. HOB skimmers are smaller and therefore less effective.

Another big benefit to in-sump skimmers is that if they ever overflow, it’s no big deal since it’s going right back into the sump instead of all over your floor.


Be aware that a lot of medications out there will cause your skimmer to go crazy and produce a lot more bubbles than usual, quickly flooding the collection cup with water. Do a quick Google search before treating with any chemical and when in doubt, turn the skimmer off.

Carbon Dosing

Because carbon dosing causes certain bacteria to become much more active, the oxygen requirements in the tank go up a lot. This requires the best aeration there is, a protein skimmer. Also, those bacteria are removed from the system by the protein skimmer. So if you are going to dose carbon, you need to run a skimmer.


My top recommendation is a Reef Octopus with DC Controllable pump.

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best protein skimmer for reef aquarium tank

If the Reef Octopus is too far out of your budget, I wouldn’t go with anything less than an Eshopps.

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