Fate and transport of solutes in heterogeneous porous media is largely affected by diffusive mass exchange between mobile and immobile water zones. Since it is difficult to directly measure and determine the effect in the aquifers, multi-tracer experiments in combination with mathematical modeling are used to obtain quantitative information about unknown system parameters such as the effective mobile and immobile porosity, and the diffusive mass exchange between mobile and immobile water zones. The Single Fissure Dispersion Model (SFDM) describing nonreactive transport of solutes in saturated dual-porosity media, has been employed as a modeling approach to explain dual-porosity experiments in the field and laboratory (column experiments). SFDM optimization with conventional methods of minimization was immensely difficult due to its complex analytical form. Thus, previous studies used a trial and error procedure to fit it to the experimental observations. In this study, a rigorous optimization technique based on the newly developed scatter search method is presented that automatically minimizes the SFDM to find the optimal values of the hydrogeologically related parameters. The new program (OptSFDM) is accompanied with an easy-to-use graphical user interface (GUI) that is flexible and fully integrated. The program usability is showcased by a few, previously presented experimental case studies, and compared against the currently available, trial-and-error based, command-line executable, SFDM code.