The Puno-Peruvian high plateau have been shaped by humans over the last 8000 years. The Waru Waru system is a direct result of the agricultural activities of the pre-Inca in the last 2000 years. The present study was conducted in the circumlacustrine zone of Titicaca (445,532 ha) near the city of Puno, Peru. The parent material of the soils originates from the Quaternary alluvial and lacustrine deposits within the high plateau with flat landscapes, and the land is used for temporary and perennial cultivation as well as extensive natural pasture. The entire region was assessed through a preliminary soil survey, based on which three soil profiles were selected as representative Waru Waru soil structures. The soil samples were subjected to morphological and physicochemical analyses and the genesis in relation to historical use was investigated. The results showed that sandy loam and clay loam textures dominate and the average sand content is 52%, giving the parent material acidic characteristics. The soils are typically covered by natural grassland, with adequate drainage conditions and the presence of a hydrological discontinuity at a depth of 60 cm. The stagnic properties of the soils are related to the seasonally wet and paleohydromorphic conditions originating from paleolacustrine conditions and flooding. The soils exhibited high variability in base content, with pH ranging from acidic to neutral and evidence of ion leaching processes and incipient concentration of salts at depth. The predominant soils were Stagnosols, Cambisols and Phaeozems in the same order (IUSS Working Group WRB, 2022), corresponding to Inceptisols and Mollisols (Soil Survey Staff, 2022a). The Waru Waru agricultural system covers an area of approximately 123,000 ha, with 5% of this area consisting of natural grasslands. The degradation of the traditional agriculture system (Waru Waru) is influenced by the socio-cultural dynamics and modernization of the agricultural sector.