Diatom, pollen, geomagnetic and geochemical analyses were carried out on a 3.6 m long sediment core taken from Lake Buyan, a highland caldera lake in central Bali Island, to reconstruct the Holocene climate changes in equatorial southern Indonesia. The core represents ∼8 thousand years sedimentation of organic-diatomaceous lake mud. Constant inclusion of benthic diatom fossils as main components indicated that suspension and inflow of littoral materials were the main sedimentary process. The core contained laminated sediments in two distinct intervals at 6.5–5.0 and 3.6–3.1 cal ky BP, and multi-proxy records showed generally drier climate in these sections especially at 3.6–3.1 cal ky BP. Lake bottom waters were more reducing condition in these laminated periods probably due to increased lake productivity by prolonged dry season and wind mixing. Laminae structures were made up of a layer composed of benthic diatoms and amorphous organic materials, and a layer made by only planktonic diatom fossils, each of which may represent rainy and dry period deposits. Although southern Indonesia shows clear Australian monsoon rainfall seasonality at present, counting of layer numbers showed interannual cycles of laminae formation. Prolonged dry seasons could obscured the rainfall seasonality in these periods, but precise depositional patterns were elusive. Unlaminated sections showed homogeneous sediment mixture of benthic, planktonic diatoms and more volume of terrigenous materials indicating wetter climate and seasonality similar to the present time. This was supported by the higher share of marsh environment pollens reflecting more stable lake level trends. The dry climate from 6.5 cal ky BP was in line with the general perception of stronger ENSO dynamics from the mid Holocene due to weaker than before boreal summer insolation, but the sporadic appearances of dry periods imply the influence of regional climate forcings such as temporal migrations of inter tropical convergence zone (ITCZ). It was, however, possible that temporal shifts of large climate mode occurred in equatorial Pacific and Indian Oceans. Wettest climate was inferred from 3.1 cal ky BP to the present and this might reflect increased importance of Austral hemisphere atmospheric convection and subsequent southerly position of ITCZ in Austral summer time.