Establishing proxies are important to fill the information gaps for environmental studies in Taylor Valley, Antarctica, where the area is sensitive to climate change and instrumental records begun only a few decades ago. This study uses molecular markers, which are compounds that preserve compositional and structural information so the sources of materials or organisms can be traced. The compounds may also be a vital membrane component that distinguishes a cellular function.

Temperature proxies based on the alkenone unsaturation indices and glycerol dialkyl glycerol tetraethers (GDGTs) are tested if these are applicable to the study area. The alkenone unsaturation indices and temperature estimates for Lake Fryxell were consistently low compared to global records and show a good potential to use as a paleotemperature proxy. Mass spectral analysis of alkenone moieties revealed the following compounds that have not been reported in the literature: octatriaconta-pentaen-2-one (C_38:5Me), nonatriaconta-pentaen-2 and 3-one (C_39:5Me and C_39:5Et), as well as tetradec-pentaen-2-one (C_40:5Me).

Based on isoprenoidal and branched GDGTs, average temperatures for the water columns of the lakes were within the error and deviations of the data, except for Lake Fryxell, where the temperatures were overestimated. The GDGT distribution patterns in present-day deposits classifies according to the different physico-chemical properties of each lake that govern oxic, suboxic or anoxic conditions in the bottom waters. This classification was successful in identifying the known paleoenvironments of the lakes.

Molecular markers were also used to trace the aviation diesel fuel and synthetic oils that were spilled when a helicopter crashed on the Lake Fryxell ice cover. Naphthalenes and n-alkanes of the fuel and C ₅ to C₆ fatty acids of the synthetic oils were biodegraded in ice associated with sediments. Volatile compounds from the diesel fuel were evaporated and water washing was a significant process that fractionated the fuel composition. Potentially, only the high molecular weight components of the synthetic oils PETs, the antioxidant tricresyl phosphates are persistent. These compounds also tend to sorb onto sediments, and may comprise the contaminants that eventually cross the ice cover and reach the pristine lake waters.