In sediments, plant biomolecules (n-alkanes and fatty acids) serve as robust proxies in paleoenvironmental studies. Although the factors controlling preservation and isotopic composition of plant biomolecules are understood in soil systems, the effect of changes in depositional environments in land-sea interfaces, especially in hypersaline environments, is not so well constrained. In this study, we observed that in bed sediments, the plant biomolecules are preserved with carbon preference index (CPI) values > 1 in high molecular weight (HMW) n-alkanes in the hypersaline, metahaline, and euhaline regions of the Pulicat lagoon, India. However, in sub-surface sediments (up to 70 cm depth), the CPI values are consistently < 1 in the hypersaline region, but > 1 in the euhaline and metahaline regions. In the hypersaline region, the alteration of plant biomolecules possibly results from halophilic bacterial degradation and fatty acid to n-alkane reduction in anaerobic conditions (pristane/phytane values < 1), during the weaker northeast monsoon (44–60 cm sub-surface). Prolonged hypersaline conditions and associated anoxia resulted in a higher isotopic difference between fatty acids and n-alkanes (δ13CFA-ALK value) in the hypersaline region (3.1 ± 1.5‰) compared to metahaline (2.2 ± 1.0‰) and euhaline (1.5 ± 1.0‰) regions. Although in the hypersaline region the HMW fatty acids have CPI values > 1, the higher δ13CFA-ALK value also suggests the alteration of fatty acids. This study suggests that if plant-derived n-alkanes are altered, the δ13C values and distribution patterns of plant-derived fatty acids should be critically evaluated before using it as an alternative proxy in coastal environments.