How To clean A Protein Skimmer

There are a couple of questions that come up all the time for those of us who deal with marine aquariums and more specifically protein skimmers on a regular basis. the biggest question is, “what is a protein skimmer?”, which I wrote about here. The next question asked most often is one that comes after someone has purchased and installed a skimmer on their tank. It is either, “how do I clean my protein skimmer”, or :how often should I clean a protein skimmer?”.

This article will answer these questions, and hopefully make the reader come out of it better equipped to deal with the ongoing maintenance of a protein skimmer. As you probably know by now, having a good skimmer is one of the single most important things you can do to improve the water quality of your tank, and maintaining that skimmer is equally as important when it comes to ongoing tank maintenance.

First of all, we have to talk about what typically happens when someone installs a new skimmer on their tank. The typical marine hobbyist first takes the easy way out, and purchases the cheapest skimmer they can afford. That ultimately turns out to be a mistake and at some point down the road they purchase a good quality skimmer. Now that they have sunk a few hundred dollars into these skimmers, they eagerly get the new unit installed and sit there staring at it, anxiously waiting for that juicy looking skimmate to start filling their collection cup.

Unfortunately, it simply does not happen like it is written above. There is a break in period for any skimmer. It is usually a couple of weeks before you can accurately judge how yours is performing. That break in period can vary, mostly depending on the quality of the skimmer you have purchased, as well as how much of a bio- load you have in your tank.

Anything you put into your tank has to become part of the environment before it will begin to be effective. this is as true of something like live rock as it is a skimmer that is made from plastic or acrylic. Anything in your system will slowly get a coating of bacteria on it that makes its surface become part of the surrounding environment. This leads to a tricky situation, since we are going to talk about how to clean a protein skimmer.

There are differing opinions on how often to clean a skimmer as well as how thoroughly to clean it. I am of the opinion that since I waited for my skimmer to become as much a part of the marine environment as it can be, I don’t want to clean it to the point that it has to re-acclimate itself all over again because this would be a never ending process. I choose to simply clean the collection cup when it is full. Depending on which tank, this can be anywhere from a few days to two weeks.

When you empty your collection cup you will have a couple of different kinds of waste to dispose of, and I would suggest that if you have a spouse you perform this task when they are NOT around. The waste you will find in your protein skimmer collection cup SMELLS!! I mean it smells really bad. When you dump the liquid portion out, the more muddy type of waste REALLY SMELLS! All I do is dump out the liquid and clean out the muddy stuff. I do not actually clean the collection cup beyond that. I want my skimmer to be able to just pick up where it left off when I took the cup off, and this is the best way I have found to accomplish this.

A good argument can be made to clean the cup more thoroughly. After all, the waste that makes it to the collection cup is already collected and riding on your bubbles, so an overly clean cup should not have a negative impact on how much waste is removed from the tank. I can buy that, but I still choose to do it the way I described. Try both ways and just go with what works for you. Neither way is right or wrong.

Most skimmers are really simple things, made up of just a plastic or acrylic tube, a collection cup, and a pump that injects both air and water into the skimmer to create the process known as foam fractionation. For all the reasons I already talked about, I do not recommend cleaning the rest of the skimmer tube unless it has accumulated noticeable debris.

When it comes to the pump, follow the manufacturers recommendations for maintenance. I have used a lot of different pumps, and I usually end up taking them out every couple of months and cleaning the impellers and air valves. Salt build up is the biggest issue here, and it can affect the number and type of bubbles your skimmer is producing, and that goes directly to how well your skimmer will work. Don’t just install your skimmer and forget about it for years.

Occasional maintenance will go a long way to extending the life of the pump and saving you some money long term. In a hobby where everything seems to be expensive, any money you can save is a job well done.