This paper is a preliminary attempt to assess the composition of pollutants in two different caldera lakes situated in the Indonesian Archipelago: Batur and Bratan. Both lakes are characterized by largely different physico-chemical regimes; Batur Lake is located in an area that is currently volcanically active, unlike Bratan Lake. The latter is much smaller and shallower than Batur Lake. The concentration of pollutants in the Indonesian equatorial lakes is largely unknown, and the impact of both biological and geothermal processes on their distribution requires attention. This study shows that the concentrations of cations (Na+
), anions (SO42−
) and trace elements (Li, B, Al, V, Cr, Mn, Co, Ni, Cu, Zn, As, Se, Rb, Sr, Mo, Cd, Sn, Cs, Ba, Pb, U, Be, Ag, Sb, Tl, Bi) differ greatly between both lakes. Most chemical parameters determined in volcanically influenced Batur Lake were tens to hundreds times higher than in Bratan Lake, and in the case of trace metals, the ratios of the two lakes’ concentrations reached several hundreds. This study also compared the composition and concentration levels of organic compounds in both lakes, such as fatty acids, halocarbons and esters. On the other hand, the content of organic chemicals in the lakes also results from biological activity by phytoplankton, zooplankton and bacteria.