Juiz de Fora is located in the hydrographic basin of the River Paraibuna, which belongs to the hydrographic basin of the River Paraíba do Sul, in the Southeast region of the country, draining areas of the States of Minas Gerais, Rio de Janeiro and São Paulo.

The city is divided among the areas of three hydrographic basins. The greatest part of the territory is drained directly by the basin of the River Paraibuna. The other two parts are in the area of the hydrographic basins of the River Peixe, to the west, and the River Cágado, to the extreme southeast, both of which are tributaries of the River Paraibuna.

The source of the River Paraibuna is on the boundary of the municipalities of Antônio Carlos and Bias Fortes, in the Serra (mountain range) da Mantiqueira, at an altitude of about 1,200 metres. The river is 166 Km long, and flows into the River Paraíba do Sul, in the municipality of Três Rios (RJ). The River has played an important role in the history of the region. It was a natural waterway which led to the first settlement there, and is a factor that has contributed to the urban growth of the city.

At first settlement took place along the main valley of the Paraibuna, occupying the flattest and widest areas on the banks of the river. Nowadays, due to the pollution caused by the release of domestic and industrial sewage produced by the city, the river no longer provides good environmental conditions for the population.

The climate in Juiz de Fora is predominantly mesothermic, with the rains concentrated in the summer period. It can be wild or moderately warm (High Altitude Tropical Climate).

There are two well-defined seasons: one with higher temperatures and more rain, from October to April, and the other from May to September, with less rain.

The average annual temperature is about 18.8ºC, February being the hottest month and July the coldest.

The average annual rainfall is 1530 mm. The month of January is the rainiest and July the driest.

With the settlement that took place along the valleys, Juiz de Fora now has almost no remains of its natural vegetation. Everything suggests that its vegetation would be classed as "semi-deciduous tropical woodland". The patches of residual forests are, therefore, secondary ones.

The relief of Juiz de Fora is hilly, having "seas of hills" with concave-convex hills. It is dissected by rivers which drain its territory. It is marked by the presence of the spurs of the Mantiqueira range to the north and those of the Serra do Mar to the south of the municipality. In the centre of the city, in the railway station, the officially registered altitude is 678m.