It borders the departments of Candelaria, Leandro N. Alem, and Apóstoles, as well as the province of Corrientes and the Republic of Paraguay, separated by the Paraná River.

The department is located on the South's peniplain, a gently undulating relief, with isolated hills of few slopes that separate the streams' courses.

To the south, the altitude increases significantly due to the proximity of the Sierra de San José, Cerro Galarza, reaching 230 meters in elevation.

The Mártires stream, which constitutes the natural boundary of the extension of the city of Posadas to the west, also presents a high degree of pollution in its lower course.

In the first semester of 2013, according to the definition used by the civil society organization TECHO, there were 72 informal settlements in the Capital Department of Misiones.