What's the difference between a protein skimmer and a filter?

Short answer

A protein skimmer removes dissolved organic compounds (DOC) by injecting fine air bubbles that bind to organics and float them out as foam. A filter (HOB, canister, sump with media) handles biological filtration, mechanical particulate removal, and chemical media. Reef tanks need BOTH; freshwater tanks generally need only the filter.

In depth

The two systems serve different roles. A skimmer is purely chemical (removes dissolved organics), a filter handles biological + mechanical + chemical filtration.

What a protein skimmer does

Injects fine air bubbles into a column of saltwater
Dissolved organic compounds (proteins, fats, dissolved fish/coral waste) bind to the bubble surface
Bubbles float up and collapse into a foam in the collection cup
You dump the foam (smelly) into the trash
Removes organics BEFORE they can break down into ammonia/nitrate

What a filter does

Mechanical: removes particles (sponge, filter floss)
Biological: hosts nitrifying bacteria that convert ammonia → nitrite → nitrate
Chemical: activated carbon removes tannins, medications, and some organics; GFO removes phosphate

Why reef tanks need both

Reef stocking densities produce more dissolved organics than biological filtration alone can keep up with. The skimmer removes organics directly; the filter (sump, refugium) handles biological conversion of any organics that escape the skimmer. In a 75+ gallon reef, running without a skimmer means accumulating organics that yellow the water and feed nuisance algae.