Large-scale inverse problems that require high-performance computing arise in various fields, including regional air quality studies. The paper focuses on parallel solutions of an emission source identification problem for a 2D advection–diffusion–reaction model where the sources are identified by heterogeneous measurement data. In the inverse modeling approach we use, a source identification problem is transformed to a quasi-linear operator equation with a sensitivity operator, which allows working in a unified way with heterogeneous measurement data and provides natural parallelization of numeric algorithms by concurrent calculation of the rows of a sensitivity operator matrix. The parallel version of the algorithm implemented with a message passing interface (MPI) has shown a 40× speedup on four Intel Xeon Gold 6248R nodes in an inverse modeling scenario for the Lake Baikal region.