Mechanical means of filtration happens when water passes through some type of filter media that catches the dirt and other particles from aquarium water. Mechanical aquarium filter media is usually the first stage in a three-stage filtration system. It acts like a strainer and catches dirt, uneaten food, fish excrement, and sludge that cannot pass through it. There are several types of aquarium filter media. The most common are sponges, filter floss, and filter pads. Aquarium gravel can also function as mechanical filter media. Sponges can also provide a bit of biological filtration since bacteria can live on their surface.

When used as the first stage in a filtration system, mechanical filtration is called pre-filtering. By removing larger and coarser particles in water, it prevents the chemical and biological aquarium filter media from getting clogged up. Chemical and biological filter media are more delicate and may not function well if clogged with large aquarium debris.