Estuaries are one of the most important ecosystems in the world, which are economically developed and densely populated. However, the intricate hydrodynamic environment and frequent human activities within estuaries have left the spatiotemporal variability of water properties in these areas inadequately understood. Recently, based on in situ observations and numerical simulations, we found significant spring-neap variability of water mass properties in the Yangtze River Estuary, which exhibited a bi-layered vertical structure. In the Yangtze River Estuary, salinity could decrease (increase) over 4 psu during spring (neap) tides in the upper layer, and satellite observations confirmed that both sea surface chlorophyll-a concentration and particulate organic carbon concentration also showed significant spring-neap variabilities. Decreasing salinity in the upper layer induced a shoreward pressure gradient force in the lower layer, which caused shoreward advection of high salinity water from the deep ocean and resulted in salinity increasing up to 2 psu in the lower layer of the Yangtze River Estuary. Dynamical diagnoses proved that spring-neap variability of water mass properties were caused by the asymmetry of tidal currents via modulating the ratio of freshwater to seawater. Similar situations also occurred in the Mississippi River Estuary. Furthermore, constructions of dams and other hydraulic projects in the watershed could greatly alter the locations with significant spring-neap water masses variability through reducing the riverine sediment flux and thus, leading to the erosion of the tidal flats in estuaries. The above results highlight the important roles of tidal asymmetry and human activities in affecting spring-neap variabilities of water mass properties in estuaries.