Characterization of karst systems, especially the assessment of structure and geometry of conduits along with forecast of state-variables, are essential for groundwater quality/quantity management and implementation/rehabilitation of large-scale engineering projects in karst regions. These objectives can be fully met by utilizing process-based discrete-continuum models, such as MODFLOW-2005 CFPv2, as employed here. However, such tools should be used with the caveat of the potential non-uniqueness of results. This research focuses on the joint-inversion of discharge, water temperature, and solute concentration signatures of Freiheit Spring in Minnesota, USA, in response to a spatiotemporally small-scale hydraulic and transport experiment. Adopting the multi-model concept to address conceptual uncertainty, seven distinctive model variants were considered. Spring hydro-chemo-thermo-graphs for all variants were simultaneously simulated, employing joint-inversion by PEST. Subsequently, calibrated models were compared in terms of calibration performance, parameter uncertainties and reasonableness, as well as forecast capability. Overall, results reveal the reliability of the discrete-continuum flow and transport modeling, even at a spatiotemporally small-scale, on the order of meters and seconds. All conceptualized variants suggest almost identical conduit tracer passage sizes which are close to the flood-pulse method estimates. In addition, the significance of immobile conduit-associated-drainable storages in karst hydrodynamic modeling, which is uniquely provided in our model code, was highlighted. Moreover, it was demonstrated that the spring thermograph and hydrograph carry more information about the aquifer characteristics than the chemograph. However, this last result can be site-specific and depends on the scale of the experiment and the conceptualized variants of the respective hydrological state.