Crowdsourced images hold information could potentially be used to remotely monitor heritage sites, and reduce human and capital resources devoted to on-site inspections. This article proposes a combination of semantic image segmentation and photogrammetry to monitor changes in built heritage sites. In particular, this article focuses on segmenting potentially damaging plants from the surrounding stone masonry and other image elements. The method compares different backend models and two model architectures: (i) a one-stage model that segments seven classes within the image, and (ii) a two-stage model that uses the results from the first stage to refine a binary segmentation for the plant class. The final selected model can achieve an overall IoU of 66.9% for seven classes (54.6% for one-stage plant, 56.2% for two-stage plant). Further, the segmentation output is combined with photogrammetry to build a 3D segmented model to measure the area of biological growth. Lastly, the main findings from this paper are: (i) With the help of transfer learning and proper choice of model architecture, image segmentation can be easily applied to analyze crowdsourcing data. (ii) Photogrammetry can be combined with image segmentation to alleviate image distortions for monitoring purpose. (iii) Beyond the measurement of plant area, this method has the potential to be easily transferred into other tasks, such as monitoring cracks and erosion, or as a masking tool in the photogrammetry workflow.