Reconstructions of past changes in algal community composition provide important context for future alterations in biogeochemical cycling. However, many existing phytoplankton proxies are indicative of individual algal groups and are not fully representative of the whole community. Here, we evaluated hydrogen isotope ratios of algal lipids (δ²H_Lipid) as a potential proxy for phytoplankton community composition. We sampled the water column of Rotsee, a small eutrophic lake in Switzerland, every second week from January 2019 to February 2020 and analyzed distributions and the relative offsets between δ²H_Lipid values (δ²H_{Lipid1/Lipid2}) from short-chain fatty acids, phytosterols and phytol. Comparing these data with phytoplankton cell counts, we found that δ²H_{C16:0 Acid/Sterol} and δ²H_{Sterol/Phytol} values reflect shifts within the eukaryotic algal community. To assess whether the selected phytoplankton groups were the main sources of the selected lipids, we further modeled algal δ²H_{Lipid1/Lipid2} values based on δ²H_{C16:0 Acid}, δ²H_Sterol and δ²H_Phytol values from batch cultures of individual algal groups and their biovolume in Rotsee and evaluated the role of heterotrophy on δ²H_{Lipid1/Lipid2} values using a model incorporating δ²H_{C16:0 Acid} and δ²H_Sterol values from microzooplankton. Annually-integrated and amount-weighted δ²H_{Lipid1/Lipid2} values measured in Rotsee were within 2 to 20 ‰ of the mean of modeled algal δ²H_{Lipid1/Lipid2} values, demonstrating a strong link with the phytoplankton community composition, while δ²H_{Lipid1/Lipid2} values including microzooplankton lipids had a larger offset. Additionally, cyanobacterial biovolume was positively correlated with the ratio of phytol and phytosterols (phytol:sterol ratio) as well as the ratio of unsaturated C18 and C16:0 fatty acids (C18:C16 ratio). Our results support the application of sedimentary δ²H_{Lipid1/Lipid2} values in eutrophic lakes as a proxy for past phytoplankton community assemblages. Moreover, the calculation of sedimentary phytol:sterol and C18:C16 ratios provides an additional proxy for reconstructing cyanobacterial blooms.