In 1989 the town was devastated by the full brunt of Hurricane Hugo, which destroyed homes, fishing boats, trees and much of the picturesque character of this historic fishing village. The stronger north side of the eyewall passed directly over the village while a Category 4 storm. Residents who took refuge in Lincoln High School, a designated storm shelter, were surprised to be flooded by a storm surge which threatened to drown all the residents. Helping one another, in pitch darkness, they were all able to get into the space above the false ceilings in the building and no one was lost.

Much of the business in the area moved westward, away from the coast, and the business district is now focused along Route 17. Many of the area residents commute northward to Georgetown or southward to Charleston for employment. McClellanville did not see another hurricane after Hugo for fifteen years. That was until 2004, when two of them, Hurricane Charley (which had devastated parts of Florida the previous day) and Hurricane Gaston hit the town in a matter of weeks, both at Category 1 strength with much less damage.

As of the censusGR2 of 2000, there were 459 people, 206 households, and 138 families residing in the town. The population density was 85.2/km² (220.9/mi²). There were 254 housing units at an average density of 47.1/km² (122.2/mi²). The racial makeup of the town was 92.59% White and 7.41% African American. Hispanic or Latino of any race were 2.18% of the population.

The median income for a household in the town was $42,500, and the median income for a family was $50,000. Males had a median income of $36,750 versus $25,781 for females. The per capita income for the town was $22,425. About 8.3% of families and 11.8% of the population were below the poverty line, including 21.8% of those under age 18 and 8.6% of those age 65 or over.