Long‐chain alkyl diols (LCDs) were applied as indicators of salinity, sea surface temperature (SST), upwelling, and nutrient conditions in marine settings. While increasing the body of most applications of LCDs proxies reconstructed paleo‐environment information, few studies reported seasonal variation in LCDs and evaluated their applicability as environmental indicators in modern marine environments. Here, the composition and distribution of LCDs in suspended particulate matter (SPM) in three seasons in the Changjiang River Estuary (CRE) were analyzed to evaluate seasonal influence on the application of LCDs as environmental indicators. We found that the reconstructed temperature based on the long‐chain diol index (LDI; LDI = C30 1,15‐diol/(C28 1,13‐diol + C30 1,13‐diol + C30 1,15‐diol)) was not consistent with satellite‐measured SST, likely due to vertical mixing of LCDs in this region. The 1,14‐diols previously used to indicate upwelling conditions, did not reflect the nutrient distribution of this region due to the Changjiang River (CR) nutrients discharge. Our results showed that the mean relative proportions of FC32 1,15‐diol (FC32 1,15‐diol = C32 1,15‐diol × 100%/(C28 1,13‐diol + C30 1,13‐diol + C30 1,15‐diol + C32 1,15‐diol)) gradually decreased from nearshore to offshore (71.1%, 37.4%, and 16.5%, respectively), suggesting that FC32 1,15‐diol was a reliable proxy for riverine input to the CRE. We found that the diol index (DI; DI = C30 1,15‐diol × 100/(C30 1,15‐diol + C32 1,15‐diol)) values were correlated strongly with salinities in spring (R2 = 0.82) and summer (R2 = 0.94), indicating that DI can be considered as a useful indicator for salinity construction in this estuary.