Banyoles (42°08′N, 2°45′E) is the largest and deepest lake of karstic–tectonic origin in the Iberian Peninsula. The lake comprises two basins and six sub-circularly shaped sub-basins fed by subaquatic springs. Periods of intense groundwater inflow in the deepest sub-basins lead to the fluidization and re-suspension of previously deposited sediments and subsequent settling forming homogenite deposits on the southern basin intermediate platforms. The multiproxy analysis of sediment cores combined with high resolution seismic stratigraphy (3.5 kHz pinger and multi-frequency Chirp surveys) allows a precise reconstruction of depositional environments and related hydrological variability and groundwater inflowduring the last ca. 7.6 cal kyr BP. According to the agemodel based on 137Cs, 210Pb and AMS 14C dating, homogenite deposition occurred between 7.2 and 5.5 cal kyr BP, stopped during the middle Holocene (5.5–2.8 cal kyr BP) and greatly increased during the last two millennia with a total of 17 homogenite layers individually up to 75 cm-thick. The onset of this unique sedimentation mode at ca. 3 cal kyr BP coincides with an increase in lake level, evidenced by the onlapping of fine-grained, distal sediments over coarser massive, carbonate-rich, littoral deposits. A detailed, multidisciplinary study of the homogenites (sedimentology, physical properties, high-resolution elemental geochemistry, mineral composition, grain-size, organic matter content and SEM) combined with seismic stratigraphy demonstrates that the fluidization events triggering the formation of the homogenites were caused by higher and more intense local groundwater inflow, related to increased rainfall during the Late Holocene and likely intensified by land use changes during the last millennium.