San Borja straddles the transition zone from flat mosaics of floodplains and forest islands, to Southwestern Amazonian Rainforest.

Like many areas in Bolivia and Latin America generally, San Borja is subject to considerable fluctuations in seasonal and annual precipitation, particularly as a consequence of climate-change related anomalies.

By road, San Borja is situated 230 kilometres (140 mi) west of the department's capital, Trinidad.

San Borja is connected towards the southwest with Yucumo situated on the road and a bus route La Paz - Yolosa/Coroico - Caranavi - Rurrenabaque.

The airport of San Borja has regular services from two airlines: Línea Aérea Amaszonas and TAM - Transporte Aéreo Militar (the Bolivian Military Airline) The town's population has increased strongly over the past three decades: In spite of high migration figures over the past decades, the city still has a noteworthy percentage of indigenous population; 17.7 percent of the San Borja Municipality population speak local indigenous languages.