Hydroclimate on ‘Uvea (Wallis et Futuna) is controlled by rainfall associated with the South Pacific Convergence Zone (SPCZ), the southern hemisphere's largest precipitation feature. To extend the short observational precipitation record, the hydrogen isotopic composition of the algal lipid biomarker dinosterol (δ²H_dinosterol) was measured in sediment cores from two volcanic crater lakes on ‘Uvea. The modern lakes differ morphologically and chemically but both contain freshwater within the photic zone, support phytoplankton communities inclusive of dinosterol-producing dinoflagellates, and experience identical climate conditions. δ²H_dinosterol values track lake water isotope ratios, ultimately controlled in the tropics by precipitation amount and evaporative enrichment. However, in 88-m-deep Lac Lalolalo a steadily decreasing trend in sedimentary δ²H_dinosterol values from −227‰ around year 988 CE to modern values as low as −303‰, suggests this lake's evolution from an active volcanic setting to the present system strongly influenced δ²H_dinosterol values. Although current hydrology and water isotope systematics may now reflect precipitation and evaporation in this lake, the interaction between these processes and large changes in basin morphology, geochemistry, and hydrology obstruct the recovery of a climate signal from Lac Lalolalo's sedimentary δ²H_dinosterol records. This work emphasizes the importance of site replication and the use of complementary climate reconstruction tools, especially when using molecular proxies that may be sensitive to more than one environmental parameter. Contrary to its neighbor, duplicate δ²H_dinosterol records from 23-m-deep Lac Lanutavake varied between −277‰ and −297‰ and indicate slightly drier conditions during the time-period known as the Medieval Climate Anomaly (MCA, 950–1250 CE). The δ²H_dinosterol signal in Lac Lanutavake was muted compared to published records from ‘Upolu (Samoa) and Efate (Vanuatu) indicating that ‘Uvea's location is not as sensitive to precipitation variability at sites farther from the SPCZ central axis. Lithogenic runoff proxies combined with δ²H_dinosterol support the interpretation of a relatively dry MCA on ‘Uvea, ‘Upolu, and Efate, potentially due to less intense precipitation, a contracted, or a more zonally oriented SPCZ.