We address the task of mapping deforested areas in the Brazilian Amazon. Accurate maps are an important tool for informing effective deforestation containment policies. The main existing approaches to this task are largely manual, requiring significant effort by trained experts. To reduce this effort, we propose a fully automatic approach based on spatio-temporal deep convolutional neural networks. We introduce several domain-specific components, including approaches for: image preprocessing; handling image noise, such as clouds and shadow; and constructing the training data set. We show that our preprocessing protocol reduces the impact of noise in the training data set. Furthermore, we propose two spatio-temporal variations of the U-Net architecture, which make it possible to incorporate both spatial and temporal contexts. Using a large, real-world data set, we show that our method outperforms a traditional U-Net architecture, thus achieving approximately 95% accuracy.