The article “Karst aquifer recharge: Comments on ‘Characteristics of Point Recharge in Karst Aquifers’, by Adrian D. Werner, 2014, Water 6, doi:10.3390/w6123727” provides misrepresentation in some parts of Somaratne [1]. The description of Uley South Quaternary Limestone (QL) as unconsolidated or poorly consolidated aeolianite sediments with the presence of well-mixed groundwater in Uley South [2] appears unsubstantiated. Examination of 98 lithological descriptions with corresponding drillers’ logs show only two wells containing bands of unconsolidated sediments. In Uley South basin, about 70% of salinity profiles obtained by electrical conductivity (EC) logging from monitoring wells show stratification. The central and north central areas of the basin receive leakage from the Tertiary Sand (TS) aquifer thereby influencing QL groundwater characteristics, such as chemistry, age and isotope composition. The presence of conduit pathways is evident in salinity profiles taken away from TS water affected areas. Pumping tests derived aquifer parameters show strong heterogeneity, a typical characteristic of karst aquifers. Uley South QL aquifer recharge is derived from three sources; diffuse recharge, point recharge from sinkholes and continuous leakage of TS water. This limits application of recharge estimation methods, such as the conventional chloride mass balance (CMB) as the basic premise of the CMB is violated. The conventional CMB is not suitable for accounting chloride mass balance in groundwater systems displaying extreme range of chloride concentrations and complex mixing [3]. Over simplification of karst aquifer systems to suit application of the conventional CMB or 1-D unsaturated modelling as described in Werner [2], is not suitable use of these recharge estimation methods.