Crop efficiency can be improved by continually monitoring their state and making decisions based on their analysis. The data for analysis can be obtained through images sensors and the monitoring process can be automated by using image recognition algorithms with different levels of complexity. Some of the most successful algorithms are related to supervised Deep Learning approaches which use a form of Convolutional Neural Networks (CNNs). In this master s dissertation, we employ supervised deep learning models for classification, regression, object detection, and semantic segmentation in crop monitoring tasks, using image samples obtained through three different levels: Satellites, Unmanned Aerial Vehicles (UAVs) and Unmanned Ground Vehicles (UGVs). Both satellites and UAVs levels involve the use of multispectral images. For the first level, we implement a CNN model based on transfer learning to classify vegetative species. We also improve the transfer learning performance by a newly proposed statistical analysis method. Next, for the second level, we implement a multi-task semantic segmentation algorithm to detect sugarcane crops and infer their state (e.g. crop health and age). The algorithm also detects the surrounding vegetation, being relevant in the search for weeds. In the third level, we implement a Single Shot Multibox detector algorithm to detect tomato clusters. To evaluate the cluster s state, we use two different approaches: an implementation based on image segmentation and a supervised CNN regressor capable of estimating their maturity. In order to quantify the tomato clusters in videos at different maturation stages, we employ a Region of Interest implementation and also a proposed tracking system which uses temporal information. For all the three levels, we present solutions and results that outperform state-of-the art baselines.