Several new tools to obtain three-dimensional information from unorganized image sets are now available for the public to use. The main advantage of this sofware, which is based in dense stereo matching, is the possibility to generate 3D content without the need of high-cost hardware (e.g. 3D scanning devices). Nevertheless, their use in real world application domains (like cultural heritage) is still not very diffused, due to the non-straightforward usability of the raw data produced. In this paper, we investigate the use of automatic dense stereo reconstruction tools for the monitoring of an excavation site. A methodology for the effective acquisition and processing of data is presented. In addition, the results of the data assessment demonstrate the repeatability of the data acquisition process, which is a key factor when qualitative analysis is performed. The use of three-dimensional data is integrated in an open source mesh processing tool, thus showing that a spatio-temporal analysis can be performed in a very intuitive way using off-the-shelf or free/open digital tools. Moreover, the use of particular rendering and the creation of snapshots from arbitrary points of view increase the amount of documentation data, and suggest a perfect integration of data produced with dense stereo matching in the future standard documentation for excavation monitoring.