Copepods vary considerably, but are typically  long, with a teardrop-shaped body and large antennae. Like other crustaceans, they have an armoured exoskeleton, but they are so small that in most species, this thin armour and the entire body is almost totally transparent. Some polar copepods reach . Most copepods have a single median compound eye, usually bright red and in the centre of the transparent head. Subterranean species may be eyeless, and members of the genera Copilia and Corycaeus possess two eyes, each of which has a large anterior cuticular lens paired with a posterior internal lens to form a telescope. Like other crustaceans, copepods possess two pairs of antennae; the first pair is often long and conspicuous.
Free-living copepods of the orders Calanoida, Cyclopoida, and Harpacticoida typically have a short, cylindrical body, with a rounded or beaked head, although considerable variation exists in this pattern. The head is fused with the first one or two thoracic segments, while the remainder of the thorax has three to five segments, each with limbs. The first pair of thoracic appendages is modified to form maxillipeds, which assist in feeding. The abdomen is typically narrower than the thorax, and contains five segments without any appendages, except for some tail-like "rami" at the tip. Parasitic copepods (the other seven orders) vary widely in morphology and no generalizations are possible.
Because of their small size, copepods have no need of any heart or circulatory system (the members of the order Calanoida have a heart, but no blood vessels), and most also lack gills. Instead, they absorb oxygen directly into their bodies. Their excretory system consists of maxillary glands.