Small endhoreic (topografically closed) lakes represent a little percentage of continental waters but, in arid or sub-arid regions, they develop special ecosystems potentially prone to ecological involution due to climatic changes. The mandatory use of light, non-invasive field techniques is often required, especially in protected areas. In the present work the use of non-invasive techniques like GPS−based bathymetric and photographic surveys have been applied to the study of two lakes, Specchio di Venere and Sfondato (Sicily, southern Italy), both natural reserves. The comparison between historical surveys and modern GPS−based bathymetries highlighted the difficulty of using the former for the reconstruction of climatic-induced variations due to the low number of measurements (spatial aliasing). In particular, at the intracaldera Lake Specchio di Venere, a high resolution survey gave new insights into a peculiar geo-ecosystem whose evolution is driven by both volcanic phenomena and biomineralization processes. On the contrary, the morphology of Lake Sfondato floor is much more simple and driven only by the superimposition of a detrital sedimentation on the initial collapse that generated the lake. The comparison betweem direct measurements and estimated changes of lake level, carried out between February 2008 and October 2009 variations, allowed us to test different hypotheses of hydrological balances, leading to opposite conclusions with respect to previous studies and remarking the fundamental importance of direct measurements in the validation of theoretical hydrological models.