This paper is devoted to the studies of clay minerals from two cores collected in the northern and central regions of the St. Anna Trough, the largest trough of the Kara Sea. The Upper Quaternary glacial, glaciomarine, and marine deposits are characterized by various contents of kaolinite, chlorite, illite, and smectite. It is established that, from older to younger deposits, the amounts of kaolinite and chlorite generally decrease, while those of illite and smectite, on the contrary, increase. A joint analysis of the distributions of clay and heavy minerals over the section allowed us to refine the position of the sources for the terrigenous matter and their temporal variability. It is shown the changes in the sources of supply were directly related to the climate changes that occurred when passing from the glacial to marine sedimentation environments.