- Males reach about 1.4 to 2.0 m (4.6-6.6 ft.) and 70 to 170 kg (154-375 lb.).
- Females reach about 1.2 to 1.7 m (3.9-5.6 ft.) and 50 to 150 kg (110-331 lb.).
Harbor seals have a rounded, fusiform (rounded in the middle and tapered at the ends) body.
Harbor seals range in color from light gray to silver with dark spots. Some are black or dark gray to brown with white rings. Spots or rings are numerous on the dorsal (back) surface and more sparse on the ventral (underside) surface. In some areas, such as San Francisco Bay, a number of harbor seals have a red or rust coloration from iron oxide deposits on their fur.
- Limbs are modified into flippers. The foreflippers, or pectoral flippers, have all the major skeletal elements of the forelimbs of land mammals, but they are foreshortened and modified.
- A harbor seal's flippers are short and webbed. Each foreflipper has five digits of about equal length.
- The foreflippers have noticeable claws. The claws are blunt and measure about 2.5 to 5 cm (1-2 in.). Harbor seals use their claws for scratching, grooming, and defense.
- Foreflippers are covered with hair.
- Foreflippers are not as broad as the hind flippers and have less resistance to water flow.
- Like land mammals, seals have five bony digits in the hind, or pelvic, limbs. The first and fifth digits are long and stout; the middle digits are shorter and thinner.
- Digits of the hind flippers are webbed. When a harbor seal spreads its hind flippers, the flippers look like wide fans.
- Like the foreflippers, the hind flippers have claws and are covered with hair.
- Harbor seals move their hind flippers side-to-side to propel themselves in water. The hind flippers also function as a rudder.
- Unlike a sea lion, a seal cannot rotate its hind flippers underneath the pelvic girdle. When on land, a seal moves by bouncing in a caterpillar like motion.
- A harbor seal has a rounded head with a fairly blunt snout.
- A harbor seal lacks external ear flaps. Its ear openings close when it dives.
- Harbor seals have 34 to 36 teeth. The front teeth are pointed and sharp, adapted for grasping and tearing (not chewing) their food. Harbor seals often use their back teeth for crushing shells and crustaceans.
- Vibrissae (whiskers) grow from the thick pads of a seal's upper lip and cheeks. Vibrissae are attached to muscles and are supplied with blood and nerves. Vibrissae continually grow throughout a seal's life.
A harbor seal has a short, flattened tail - tucked between its hind flippers.
- Harbor seals have thick, short hair. The coat is made of coarse guard hairs and finer, but denser underhairs. Each guard hair has three to six underhair fibers attached to the root.
- The density of a harbor seal's hair increases with age.
- Glands in the skin secrete oil which helps waterproof the hair.
- The hair provides no insulation for the harbor seal.
- Harbor seals molt (shed their hair) each year after the breeding season. They gradually lose their hair in patches. Molting generally lasts one to two months.
- Females molt after their pups are weaned. In fertilized females, hormonal changes at the end of the molt may trigger blastocyst implantation and embryo development.
- Pups shed a white coat called lanugo shortly before or after birth. They do not molt again until they are a year old.
- Based on observations in zoological environments, harbor seals generally seem to decrease their food intake during molting.