Carbonates are the main components of Iberian Quaternary lake sediments. In this review we summarize the main processes controlling carbonate deposition in extant Iberian lakes located in Mesozoic and Tertiary carbonate-dominated regions and formed through karstic activity during the Late Quaternary. The lakes, relatively small (1 ha to 118 ha) and relatively shallow (Zmax = 11 to 40 m) provide examples of the large variability of sedimentary facies, depositional environments, and carbonate sources. Hydrology is dominated by groundwater inflow except those directly connected to the fluvial drainage. Nine lakes have been selected for this review and the main facies in palustrine, littoral and profundal environments described and interpreted.