The Fourier transform-Raman spectra of two lacustrine sediment cores from Antarctic sites are reported. The Lake Hoare specimens were predominantly calcium carbonate, quartz and β-carotene, with chlorophyll and calcium sulphate being noted as minor components. No evidence was found for iron (III) oxide or oxy-hydroxide bands. The Lake Nella specimens, in contrast, contain chlorophyll and quartz predominantly, but the absence of β-carotene is noteworthy. Here, the presence of haematite and a haematite–goethite mixture have been identified, with weaker features such as those of scytonemin, characteristic of cyanobacterial mats. The Raman spectra indicate that two different types of lake chemistry have been operating and several reasons are proposed for this.