This work deals with a semilinear system of parabolic partial differential equations (PDEs) on an unbounded domain, related to environmental pollution modeling. Although we study a one-dimensional sub-model of a vertical advection–diffusion, the results can be extended in each direction for any number of spatial dimensions and different boundary conditions. The transformation of the independent variable is applied to convert the nonlinear problem into a finite interval, which can be selected in advance. We investigate the positivity of the solution of the new, degenerated parabolic system with a non-standard nonlinear right-hand side. Then, we design a fitted finite volume difference discretization in space and prove the non-negativity of the solution. The full discretization is obtained by implicit–explicit time stepping, taking into account the sign of the coefficients in the nonlinear term so as to preserve the non-negativity of the numerical solution and to avoid the iteration process. The method is realized on adaptive graded spatial meshes to attain second-order of accuracy in space. Some results from computations are presented.