Confocal laser scanning microscopy is a useful nondestructive approach for the visualization of fluorescent reporters in planta. Samples are usually placed between a slide and a cover slip which, although suited to single time-point imaging, does not allow long-term observation. Here, we describe a technique to monitor changes in fluorescence in the Arabidopsis root over a long period of time. Treatment can easily be performed, and this approach is suitable for use in low-throughput chemical screens. We also present a rapid method to analyze fluorescence intensity profiles generated using this protocol.