Approaching rock art as one of many elements of greater, complex natural systems allows for a better understanding of rock art panels as dynamic realities. This stands in contrast to the traditional concept in which rock art is framed as a static set of paintings and/or engravings over a rock surface. The nature of the rock surface, and even other elements related to the supporting rock, such as the network of microfissures or the very composition of the rock, have generally been of secondary interest. Information on the environmental conditions, even at the most basic level, has been absent, as has the nature (or even the mere presence) of the biological communities harboured by the supporting rock. This new, dynamic, concept of rock art, needs to be understood by means of empirical data, in which quantitative and non-contact methods are of particular use. This paper deals with the application of digital image analysis (Principal Component Analysis and digital classification algorithms) as the basis of several research strategies for identifying these elements, measuring their extent, and monitoring the effects of these elements over time. It also presents the advantage of freely available software, minimising the overall cost of the analyses. Some examples were performed in laboratory conditions, and others in subterranean environments such as Roman hypogean tombs and Altamira Cave.