Epikarst springs are critical discharge pathways in shallow karst groundwater systems, yet their runoff processes and water source heterogeneity remain poorly understood in well-developed epikarst zones. Previous research has focused primarily on weakly developed epikarst, lacking insights into the complex hydrogeological functions under multi-conduit media. Conducted in the Huajiang Valley, a representative karst region in Southwest China, this study integrated continuous monitoring of 18 epikarst springs—tracking rainfall, air temperature, electrical conductivity (EC), water temperature, and water level—to analyze rainfall response patterns and water source differentiation, with emphasis on the efficacy of water temperature as a high-sensitivity tracer. The results reveal that epikarst springs in well-developed zones exhibit complex water sources (up to six distinct contributors), dominated by conduit flow (3.90–79.06%), fracture flow (3.01–68.90%), interlayer solution fissure flow (4.17–69.38%), and matrix flow (2.15–59.06%), while rainfall (1.03–22.50%) and slope runoff (0.69–6.22%) play lesser roles. Rainfall events induced differentiated hydro-thermal responses with significant time-lag effects: springs with more complex sources showed longer delay times (average lags of 73.99h, 27.67h, 42.35h, 49.22h, and 53.67h for 2–6 sources, respectively). Water temperature tracing identified 1–4 water sources and revealed seasonal variations in over 70% of the springs, with dual sources dominating in spring, multi-source mixing in summer, and the highest differentiation during autumn events. Strong consistency between EC and water temperature methods confirms that water temperature can effectively replace or supplement conventional tracing techniques. These findings reflect a hydrogeological regime characterized by multi-source dominance, short duration, and pronounced heterogeneity, underscoring the unique advantage of water temperature tracing in elucidating hydro-thermal coupling processes in karst systems.