Considered as the second smallest in the metropolis, the population of San Juan exhibited a downward trend. From 126,708 inhabitants in 1990, the city’s total population slid to 120,752 in 2002 or a reduction of 4.7%. As a matter of fact, from 1990 onwards, an annual decline in the population has been observed, averaging at 0.39%. This was a stark contrast to the city’s total population of 129,833 in 1980, whose growth was attributed to both migration and natural increase. The town’s total population represents 1.2% of the region’s total.
While a drop in the town’s population was reported, increases in the number of inhabitants were registered in some of its barangays. From the year 2000 to 2002, population growths were reported in eight barangays, with barangay Rivera and St. Joseph registering the biggest growth rates of 26% and 21%, respectively. Other barangays, which exhibited increases in population, include Greenhills, Sta. Lucia, San Perfecto, Salapan, Progreso and Isabelita.
Although San Juan’s total population decreases, its population density on the other hand, rises. Population density is the number of persons per unit of area. From 21,323 persons per square kilometer in 1990, the town’s population density rose to 21,063 persons per square kilometer in 2003.
This indicates that San Juan is becoming less densely populated as the number of people, who live on each square kilometer of its total land area, has reduced to 21,063 persons per square kilometer in 2003 from 21,323 persons per square in 1990.
Of the city's total population, 53% or 64,537 are males while 47% or 56,215 are females.
The population of San Juan is relatively young. 27% or 32,165 people of the town’s inhabitants belong to the age bracket under 1-14 years old.
Aside from the San Juan River which runs along the western order of the municipality, two narrow creeks outline the north western and south western borders of San Juan. The Ermitaño creek from the northern border of Barangay Pasadena near the creek are also visited by floods due to the presence of the creek.
Maytunas creek, on the other hand, runs along the southern border of the municipality but hardly causes flooding on the surrounding areas.