After lighting, protein skimmers are probably the most talked about piece of equipment for marine/reef aquariums.

In this short article, we're going to breakdown the dos and don'ts of protein skimming. Whether you're shopping for your first protein skimmer or looking to upgrade to a new model, the best practices listed below will help you shop, set up and maintain your skimmer so your tank can reap the maximum benefits.

We'll begin by explaining what a protein skimmer is and what benefits it can provide for your aquarium.

Protein Skimmer Overview

A protein skimmer is a piece of filtration equipment designed to remove dissolved organics from aquarium water. To accomplish this feat, very small bubbles are generated inside the skimmer body. Dissolved organics are attracted to the bubbles and "stick" to them as they rise into a collection cup for easy removal. The waste inside the collection cup is called skimmate.

Now, you may be asking yourself how all this magic happens.

Most of the dissolved organics inside our aquariums are amphipathic or amphiphilic. One part of the molecule is attracted to water (hydrophilic) and one part is repelled by water (hydrophobic). These properties cause the molecules to be attracted to surfaces where air and water meet. This can occur at the surface of your aquarium but hopefully more so in the skimmer itself. Running a protein skimmer as a part of your marine aquarium's filtration system will help reduce nutrient levels to improve water quality.

Now that you know how a protein skimmer works and what it can do for your tank, let's dive into the dos and don'ts of protein skimming.


  1. Do buy the correct type of skimmer for your aquarium. If you don't have a sump, don't buy an in-sump skimmer! It sounds simple enough, but we run into this situation a lot with customers. Be sure to read the product descriptions of the protein skimmers you are considering closely to be certain you're buying the right style for your tank (hang-on, in-tank, in-sump or external).
  2. Do research to find out the best protein skimmers within your budget. There are many moderately priced skimmers that will perform very well for years to come. Read the protein skimmer product reviews written by hobbyists like you on our website to learn what your peers like or dislike about the models you are considering.
  3. Do allow your protein skimmer time to "break in". New skimmers frequently don't produce a lot of skimmate during the first week or two they are set up. Sometimes they have almost the opposite effect, foaming like crazy and filling the collection cup with clear liquid. To counter this, rinse the skimmer thoroughly with lukewarm to hot water to remove dust or residual oils left over from the manufacturing process. New skimmers frequently don't produce a lot of skimmate during the first week or two they are set up. Sometimes they have almost the opposite effect, foaming like crazy and filling the collection cup with clear liquid. To counter this, rinse the skimmer thoroughly with lukewarm to hot water to remove dust or residual oils left over from the manufacturing process.
  4. Do clean your protein skimmer at least once per week (or follow manufacturer guidelines) to ensure the skimmer is working at its full potential. Clean and/or drain the collection cup as needed. Don't neglect cleaning the pump and impeller to prevent reduced flow or premature failure.
  5. Do buy a protein skimmer that is rated for a larger aquarium than you actually have. For example, if you have a 100 gallon tank, don't buy protein skimmer that is rated for aquariums "up to 100 gallons." You want a protein skimmer that you know will be efficient enough to handle your system as it continues to grow. You should also take into account your aquarium's bioload and your own maintenance habits when considering a skimmer. Bottom line: you are better off buying a skimmer rated for a larger tank than a smaller one.
  6. Do keep the water in your aquarium or sump where the protein skimmer is located level at all times. If the water level fluctuates too much, it can affect the skimmer's production. The use of an auto-top off system helps keep salinity constant and skimmate production steady.
  7. Do ask questions. It doesn't matter which type of skimmer you use, there is always the potential that problems may arise that you can't figure out how to solve on your own. Chances are fellow hobbyists have combated the same situations you'll face owning a protein skimmer. If you're interested in modding your skimmer or would like help getting rid of micro bubbles, feel free to contact us or hit up your favorite forum for a solution.


  1. Don't buy a "cheap" or undersized protein skimmer as a quick fix or band-aid. If you're considering buying a protein skimmer that you'll replace in 6 months anyway, just be patient and purchase a more powerful, properly sized unit when you can. Buying the right equipment the first time is always the way to go.
  2. Don't neglect the maintenance of your protein skimmer. Venturis get clogged, impellers get covered in gunk, the walls of your skimmer will be splattered with organic matter and skimmer cups need to be cleaned. Don't make your livestock suffer—stay regular with maintenance and your aquarium will reap the rewards that come from clean water.
  3. Don't buy a protein skimmer that is TOO LARGE. It seems contrary to "Do #5," but what we mean is don't go overboard by purchasing a protein skimmer rated for 150 gallon tank when your aquarium is only 16 gallons. Sure, you might get some skimmate production, but there likely won't be enough dissolved organics for the skimmer to function properly. Plus you don't want to waste precious space or electricity that can be used to accommodate other equipment.
  4. Don't use tap water conditioners or two-part epoxies while your protein skimmer is on. Tap water conditioners can have a soapy effect in water that prevents protein skimmer bubbles from popping like normal. The soapy conditions and synthetic slime coat formed on fish may cause the skimmer to act crazy. Using two-party epoxies while your skimmer is running can cause similar problems. The best way to prevent this from happening is to shut down your skimmer temporarily and perform a water change after usage.
  5. Don't make too many changes in your protein skimmer settings too quickly. It takes time for adjustments to take effect. For example, if you change the water level or collection cup height, you should allow a day or two to see how the skimmer's performance has changed. If your skimmer is overflowing and spewing clear liquid, by all means, readjust the settings. Otherwise just sit back for a day and let the new settings get dialed in before make additional changes.

Hopefully this article has provided you with a better understanding of the dos and don'ts of protein skimming. If you have your own dos and don'ts to share, please leave them in a comment below. We'll add the best tips into the article to enrich it for future readers.

If you have questions about protein skimmers, do not hesitate to contact us. We can help you choose your first skimmer and guide you through installation step-by-step. We've also written several more articles about protein skimmers that you may find useful. We've included hyperlinks to them below.