The purpose of this paper is to demonstrate possibility of the structural evaluation of ecological systems by a factor analysis technique. We have chosen a real data set characterizing an agro-ecological system in region of Dolna Krupa to extract significant factors of the ecosystem and to analyse the most important relationships between the factors. The basic soil and agricultural data set has been completed by hydrometeorological and radiological data. The data have related to a time period of 16 years (1973 - 1989). We have applied to this set an exploratory factor analysis method based on the single value decomposition technique and the abstract rotation by varimax. A latent structure of the ecosystem obtained from the analysis has consisted of several factor sets on various latent levels. This hierarchy arrangement of ecosystem structure allows one to evaluate the parallel and serial relationships inside the analysed system. Analysis results indicate an advantageous facility of the computational approach mainly for sufficiently large input data sets.