The establishment of effective proxies for the differentiation of sedimentary facies in the tide-dominated river mouth is fundamental to the delineation of stratigraphy and the study of paleoenvironments. Geochemical signatures of the acetic acid (HAc) extractive phases of alkaline earth metals, such as Sr, Ba, and Ca, are closely related to sedimentary environments and thus provide a novel method for discriminating the sedimentary facies of river mouth. In this study, 50 surface water and surface sediment samples were obtained from different geomorphological units of the Jiulong River mouth, i.e., river channel, distributary channel, delta front, delta front slope, prodelta, and shallow marine area, and the salinity of the water, the grain size, and the Sr, Ba, and Ca contents and Sr/Ba ratio in HAc leachates of the sediments were determined. Contents of alkaline earth metals in HAc leachates of surface sediments from the Yangtze coast were also collated. The goals of this study were to reveal the spatial distribution of alkaline earth metals in the Jiulong River mouth, define their depositional mechanisms, and search for effective geochemical proxies for identification of the various sedimentary facies in the fluvial to marine transition zone. The results revealed several land-to-sea gradients. The Ba content decreased rapidly from the distributary channel to the sea, and the Sr and Ca contents and Sr/Ba ratio increased gradually with the increase in salinity. Salinity, marine biomass, and sedimentary dynamic processes, were speculated to be the main reasons for the differences in their spatial distributions. There were significant differences in Ba, Sr, Ca, and Sr/Ba between the river channel and the distributary channel, in Ca and Ba between the distributary channel and the delta front (slope), and in Sr, Ca, and Sr/Ba between the delta front (slope) and the prodelta–shallow marine region. The Sr–Ba scatterplot showed that the sediments of the river channel and alluvial plain were located as a high Ba and low Sr element-defined end-member, whereas samples of the prodelta and shallow marine formed a high Sr and low Ba end-member. These can be used as characteristic end-members indicating terrestrial facies and marine facies, respectively. The sediments of the delta plain, tidal river, distributary channel, delta front, and delta front slope are located between these two end-member regions of the scatterplot, and this region of the diagram can be used to identify land–sea transitional sedimentary facies.