As of the census of 2000, there were 12,950 people, 4,598 households, and 3,034 families residing in the city. The population density was 695.7 people per square mile (268.7/km²). There were 5,080 housing units at an average density of 272.9/sq mi (105.4/km²). The racial makeup of the city was 69.41% White, 25.14% African American, 0.32% Native American, 1.07% Asian, 0.12% Pacific Islander, 1.98% from other races, and 1.96% from two or more races. Hispanic or Latino of any race were 4.39% of the population.

There were 4,598 households out of which 31.8% had children under the age of 18 living with them, 47.6% were married couples living together, 14.9% had a female householder with no husband present, and 34.0% were non-families. 28.6% of all households were made up of individuals and 10.2% had someone living alone who was 65 years of age or older. The average household size was 2.37 and the average family size was 2.90.

In the city the population was spread out with 21.6% under the age of 18, 19.5% from 18 to 24, 28.9% from 25 to 44, 17.8% from 45 to 64, and 12.2% who were 65 years of age or older. The median age was 30 years. For every 100 females there were 114.3 males. For every 100 females age 18 and over, there were 117.6 males.

The median income for a household in the city was $36,532, and the median income for a family was $42,894. Males had a median income of $22,465 versus $23,474 for females. The per capita income for the city was $20,501. About 11.5% of families and 13.0% of the population were below the poverty line, including 20.3% of those under age 18 and 11.1% of those age 65 or over.

Beaufort is the center of an urban cluster with a total population of 46,227 (2000 census), comprising the city and its surrounding towns and unincorporated areas including Port Royal, Burton, Lady's Island, Shell Point, Laurel Bay, and Parris Island, among others.

Beaufort is also part of the larger Hilton Head Island-Beaufort Micropolitan Statistical Area which includes Beaufort and Jasper counties and had a total population of 159,247 in 2005 (U.S. Census Bureau estimate). According to the more detailed data available in the 2000 census, the population included in this micropolitan area (which actually was designated after the census itself) was 64% urban and 36% rural. It included the urban clusters of Beaufort (2000 pop.: 46,227), Hilton Head Island (34,400), Bluffton (6,136), and Ridgeland (3,585).