The datasets comprise stable isotope, pollen abundance and lipid biomarker data that we analysed in sediments from the Fern Gully Lagoon wetland (Latitude 27.4174°S, Longitude 153.4600°E, elevation of 39 m above sea level), North Stradbroke Island (also known as Minjerribah), Australia. Two overlapping nine-metre cores were obtained in April 2015 using a modified Livingstone-Bolivia square-rod piston-corer. Cores were aligned using CPLSlot sequence plotting software. The sedimentary record spans the last ~210 kyrs. We analysed total organic carbon and total nitrogen contents of the sediments. We also determined the d13C and d15N composition of the organic matter present in the sediments. Errors of these parameters were also included. The analyses werer undertaken on a EuroVector EuroEA elemental analyser, in-line with a Nu Instruments Nu Horizon continuous flow isotope ratio mass spectrometer (EA-IRMS). Pollen abundance data were also included as relative percentages of rainforest vs herbs and grasses vs sclerophyll vegetation relative to the total terrestrial pollen found in each sample. Charcoal content was also included. Lipid biomarker data comprise key paramters such as the carbon preference index (CPI), average chain length of C27-C33 n-alkanes with (ACL), Paq index, concentration of C31 ab-hopane and as ratio with major plant sterols [C31hopane/(sitosterol+stanol+stigmasterol+stanol)] and GDGT-based temperature and pH indices and on their basis estimated temperature and pH values of the studied samples. The biomarker extracts and fractions were analysed by gas chromatography mass spectrometry (GC-MS). This study is an extension and evaluation of previous work reconstructing regional interglacial climate history at Fern Gully Lagoon (Kemp et al., 2020, 2021), seeking to understand the influence of temperature and wetland surface area on the palaeoclimate record. As previous climate inferences include a degree of uncertainty due to the possible human impact on terrestrial vegetation, we utilise a wide range of climate proxies preserved in this wetland to characterise sources of organic matter and determine vegetation water stress. In addition, we quantified mean annual air temperatures (MAAT), potentially allowing temperature-driven vegetation changes to be identified. To reconstruct changes in wetland surface area resulting from increased drying, we use a combination of simple basin morphology and the age-depth model to study the impact on evaporation-driven vegetation moisture stress on wetland size.