The southeastern Fennoscandian Shield is a specific region dominated by glacial and periglacial originated Quaternary deposits. In dense boreal vegetation zones, direct remote decoding of Quaternary sediments is impossible. Our aim is to assess the efficiency of machine learning algorithms for identification of types of Quaternary deposits based on spectral data of vegetation cover and digital elevation model data. A comparative analysis of two classification methods, discriminant analysis (DA) and classification and regression trees (CARTs), was performed. Two models, DA and CART, were constructed based on a set of spectral variables. They included principal components and spectral indices, such as the normalized difference vegetation index, the normalized difference moisture index, and the clay minerals ratio. When the absolute height and the topographic position index (DA+ and CART+ models) are added to a set of independent variables, the classification of Quaternary sediments becomes more accurate. The nonparametric CART method was shown to be more accurate in differentiating loose deposits. The correctness of the CART+ model for the reference sample of observation points was as high as 90.5%. According to the trained data, mapping of Quaternary deposits was carried out. Kappa analysis showed that the agreement with the map of Quaternary deposits for the CART+ and DA+ models was 0.5 and 0.44, respectively. For the DA and CART models, the agreement was much lower. It is noted that the sets of spectral data for the vegetation cover more clearly show the grain-size composition of loose sediments. To make the classification of Quaternary deposits more correct, morphometric indicators were added. Furthermore, the CART+ method was used to estimate the maximum height of glaciolacustrine sediments (117.5 m), which corresponds to the maximum absolute mark of the periglacial reservoir.