Climate is one of the key factors controlling sediment accumulation in lacustrine ecosystems. Integrated studies of continuous lake-sediment cores, including radiocarbon dating, grain-size analysis, mineralogical and chemical characterization, and measurements of magnetic properties, enable reconstructions of sedimentation conditions during the Late Quaternary. Such studies are particularly relevant for lakes of the Southern Urals, which are located near a climatic divide and for which episodes of increasing/decreasing moisture have been interpreted inconsistently. This paper presents data on the age, material composition, and genetic features of bottom sediments from lakes Bolshoye Miassovo and Maloye Miassovo. The results show that, based on grain-size distribution, mineral composition, and inorganic geochemistry, the studied lacustrine sediments exhibit a pattern typical of freshwater lakes – the predominance of allothigenic silt-sized particles. This is supported by the structure of allothigenic-input factor F1 derived from factor analysis. Quaternary deposits represented by eluvial, slopewash, colluvial, and alluvial facies were identified as the main source of allothigenic material for the investigated basins. The ICV index and the A-CN-K diagram indicate that the sediments formed predominantly from stable allothigenic minerals of the primary sedimentation cycle, sourced mainly from Quaternary deposits and exposed pre-Quaternary rocks. The transport pathways of allothigenic material are linked to the directions of slope flows and channel networks visible on the Quaternary-deposit map. The integrated analysis allowed us to identify the most informative proxies and to correlate them with global and regional climatic stages and events, including the Bølling warming (~14,700 cal. yr BP), the ~8200 cal. yr BP cooling event, aridization in the Southern Urals (~2000 cal. yr BP), and Bond Event 1 (~1500 cal. yr BP). Additional climate-arid events were identified at ~11,430, ~6100, ~4250, ~3537, and ~1065 cal. yr BP.