Similar to any other geophysical method, seismic refraction method faces non-uniqueness in the estimation of model parameters. Recently, different nonlinear seismic processing techniques have been introduced, particularly for seismic inversion. One of the recently developed metaheuristic algorithms is bat optimization algorithm (BA). Standard BA is usually quick at the exploitation of the solution, while its exploration ability is relatively poor. In order to improve exploration ability of BA, in the current study, a hybrid metaheuristic algorithm by inclusion a mutation operator into BA, so-called mutation based bat algorithm (MBA), is introduced to inversion of seismic refraction data. The efficiency and stability of the proposed inversion algorithm were tested on different synthetic cases. Finally, the MBA inversion algorithm was applied to a real dataset acquired from Leylanchay dam site at East-Azerbaijan province, Iran, to determine alluvium depth. Then, the performance of MBA on both synthetic and real datasets was compared with standard BA. Moreover, the dataset was further processed following a tomographic approach and the results were compared to the results of the proposed MBA inversion method. In general, the MBA inversion results were superior to standard BA inversion and results of MBA were in good agreement with available boreholes data and geological sections at the dam site. The analysis of the seismic data showed that the studied site comprises three distinct layers: a saturated alluvial, an unsaturated alluvial, and a dolomite bedrock. The measured seismic velocity across the dam site has a range of 400 to 3,500 m/s, with alluvium thickness ranging from 5 to 19 m. Findings showed that the proposed metaheuristic inversion framework is a simple, fast, and powerful tool for seismic data processing.