The Jinan karst spring system, discharged by 108 springs in 2.6 km2 city center area of Jinan, China, has been suffering lower regional groundwater levels, which threatens the karst springs outflowing and aquatic ecological civilization. For better spring protection, monthly hydrogeochemical and isotopic investigations were conducted in four representative karst springs (Baotu Spring (BTQ), Heihu Spring (HHQ), Zhenzhu (ZZQ), and Wulongtan Springs (WLT)) in 2016. Results showed that the BTQ, WLT, and ZZQ had similar hydrogeochemical and isotopic behaviors, which were different with that of HHQ. By combining the daily water level data with monthly hydrogeochemical and isotopic data of BTQ and HHQ, the hydrogeological processes of the two neighboring karst springs (470 m apart) are distinguished. (a) BTQ is recharged by two sources of precipitation and river water, while HHQ is recharged mainly by precipitation. (b) Hydrogeochemical characteristics of Baotu Spring are mainly controlled by calcite, dolomite, and gypsum dissolution mixture with river water and agricultural activity, while the hydrogeochemical characteristics of Heihu Spring are mainly controlled by calcite, dolomite, and gypsum dissolution in dry season, and dilution in wet season. (c) The discharge component of both springs is storage water by diffuse flow which is pressured by new infiltration rain water. The ratio of rain water is 14% in Baotu Spring and 9% in Heihu Spring calculated by a binary mixture model. Overall, this study puts forward the standpoint that neighboring karst springs with the same geological condition, can show different hydrogeological characteristics, which is a useful evidence for understanding the heterogeneity/complexity of karst aquifers.