It is located in a small valley, 5 miles (8 km) southeast of downtown San Salvador.

Most of San Marcos is a residential suburb with many middle-income and low-income dwellings.

The city is the main gateway for air travelers because it is bordered by the Comalapa Highway (RN-5 (Autopista Comalapa)), the freeway that connects El Salvador International Airport with San Salvador.

Not much commerce exists outside the municipal public market and the southeast bus station, however, there is a significant textile industry in the San Marcos Free Trade Zone, and logistic/distribution companies along the Comalapa Highway.

The city's per capita GDP(PPP) is US $5,480 and it has a Human Development Index of 0.759 as of 2002.