Weed management is one of the most important aspects of crop productivity; knowing the amount and the locations of weeds has been a problem that experts have faced for several decades. This paper presents three methods for weed estimation based on deep learning image processing in lettuce crops, and we compared them to visual estimations by experts. One method is based on support vector machines (SVM) using histograms of oriented gradients (HOG) as feature descriptor. The second method was based in YOLOV3 (you only look once V3), taking advantage of its robust architecture for object detection, and the third one was based on Mask R-CNN (region based convolutional neural network) in order to get an instance segmentation for each individual. These methods were complemented with a NDVI index (normalized difference vegetation index) as a background subtractor for removing non photosynthetic objects. According to chosen metrics, the machine and deep learning methods had F1-scores of 88%, 94%, and 94% respectively, regarding to crop detection. Subsequently, detected crops were turned into a binary mask and mixed with the NDVI background subtractor in order to detect weed in an indirect way. Once the weed image was obtained, the coverage percentage of weed was calculated by classical image processing methods. Finally, these performances were compared with the estimations of a set from weed experts through a Bland–Altman plot, intraclass correlation coefficients (ICCs) and Dunn’s test to obtain statistical measurements between every estimation (machine-human); we found that these methods improve accuracy on weed coverage estimation and minimize subjectivity in human-estimated data.