The article considers the study results of composition, microstructure and physical-chemical properties of the quaternary clays of the Prikhankayskaya depression in district of the lake Khanka (Primorye) on the example of air-dry samples of geological borehole 45-b in the range of 18–62 m. The objective of research was to obtain new information about the properties of widespread clay sediments in this area using geologic-lithological materials and laboratory data. The schematic geologic-lithological column was composed with the selection of various zones in the quaternary clay sediments section and the border with sediments of the Neogene System. The methodological scheme of laboratory studies of clays was proposed. This scheme includes the determination of chemical and microelement composition, clay minerals, contents of carbonates, water-soluble salts, mobile forms of aluminum oxide, humus, as well as microstructural parameters (method «Microstructure») and some physical-chemical properties. Geochemical coefficients (Kz, CIA, CIW, ICV) determined the degree of chemical maturity of clays and confirmed the results of palynological studies reflecting the fluctuations of the climatic conditions of their formation. For the group of toxic microelements for the first time the special indicator (Zc) was calculated. Which was the criterion for a degree of pollution of the clay sediments section. Clay minerals of the quaternary clays are represented by smectite and hydromica. The clear change in the mineral association was found when passing to the Neogene sediments (kaolinite prevails). The method «Microstructure» revealed the aggregated type of clays microstructure, the domination of the particles of coarse dust fraction among the primary (free) particles and the almost complete absence of the particles of fine-grained sand fraction, the participation of various fractions in the composition of aggregates. The variants of the formation of certain types of aggregates (on sizes) in the fluviolacustrine «khankayskiy» clays are presented. Solid part density, water resistance (soaking time), sedimentation volume, plasticity, relative swelling (samples-pastes) were determined using standard methods for clays. By special methods, the cation exchange capacity was measured and the calculated values of the plasticity index were obtained from forecasting formulas using the yield limit. The proposed methodological scheme of complex laboratory studies of clay sediments can be recommended for problematic geologic-lithological and engineering-geological sections.