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Groundwater is a vital resource in the Chuoshui River alluvial plain (CSAP), a key agricultural area in Taiwan. Understanding groundwater recharge is crucial for sustainable water management amidst changing climatic conditions and increasing water demand. This study investigates the major ion composition, solute Sr concentrations, and ⁸⁷Sr/⁸⁶Sr ratios in groundwater and stream water from the Choushui River (CSR) to trace groundwater recharge sources. The Piper diagram reveals that most groundwater samples are of the freshwater Ca–HCO₃ type, aligning with the total dissolved solids (TDS) classification. TDS and major ion compositions indicate that groundwater near Baguashan Terrace (BGT) and Douliu Hill (DLH) primarily derives from stream water and rainwater. Na⁺ and Cl⁻ enrichment in some aquifers of BGT and DLH is attributed to the dissolution of paleo-sea salt and mixing with paleo-seawater from sedimentary porewater. Elevated dissolved Sr concentrations and lower ⁸⁷Sr/⁸⁶Sr ratios in these aquifers further support the intrusion of paleo-seawater. Groundwater in the proximal fan shows high TDS due to intensive weathering, complicating the use of TDS as a tracer. Sr isotopic compositions and solute Sr²⁺ concentrations effectively distinguish recharge sources, revealing that the CSR mainstream primarily recharges the proximal fan and BGT region, while CSR tributaries and rainwater mainly recharge the DLH region. This study concludes that Sr isotopic compositions and solute Sr²⁺ concentrations are more reliable than TDS and major ion compositions in identifying groundwater recharge sources, enhancing our understanding of groundwater origins and the processes affecting water quality.