Carbonate aquifers are critical for the health and well-being of human communities. Despite considerable efforts on the structure of karst aquifers, the variable and invisible flow paths or the vertical and spatial heterogeneity of karst systems remain too complex to be fully understood. An artificially constructed small limestone aquifer with an extensive network of observation wells in the Miyako Island, Japan, provides a unique opportunity to illustrate the vertical and spatial hydrological connectivity for water movement and storage. Water chemical data at two different depths over six years, including electrical conductivity (EC), dissolved oxygen (DO), oxidation–reduction potential (ORP), major ions (Na+, K+, Ca2+, Mg2+, SO42−, and HCO3−), δ18O and δ2H capture water mixing processes during groundwater recharge in the aquifer influenced by irrigation pumping and recharge by precipitations throughout drying and wetting cycles. Results suggest that the intensive weathering of coral limestone under the impact of agricultural fertilization, as indicated by high EC values and high concentrations of Ca2+ and HCO3−. The high DO and low ORP values imply a lack of organic decomposition activity, which is typical in the karst groundwater condition. More importantly, groundwater recharge in the small aquifer was found to be influenced by following three processes. Spatially, both Cl− and NO3−−N indicate the large heterogeneity of water mixing as rainfall or drainage water percolates differently to various parts of the aquifer. Vertically, there are apparent differences in the concentration of Cl− and NO3−−N between the top and bottom layers in several wells, suggesting that, even within a single well, the vertical profile can be weakly connected between the top and the bottom layers. The bottom layer should have been recharged by lateral water inflow from fractures or conduits. And thirdly, the even distribution of Cl− over the long precipitation season from October 2016 and March 2021 and another nearly even distribution of NO3−−N in the low fertilization season in March 2021, demonstrate that the aquifer system is basically connected and porous. In summary, the insights gained from our study reveal that: 1) coral limestone can be treated as a well-developed porous aquifer and 2) the hydrological connectivity is highly heterogeneous and influenced by rock properties, including formation structure, degree of weathering, and clay content. Such findings are essential for understanding the hydrogeological properties of coral limestone aquifers globally.
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