1. A computer method for forecasting characteristics that can be approximated by mass concentration of a tracer in an incompressible fluid comprising: (a) defining, by use of a specially-programmed computer, a 2D spatial grid for an area of interest in the incompressible fluid; (b) defining, by use of the specially-programmed computer, a 3D spatial grid based on the 2D spatial grid and bathymetric data; (c) defining, by use of the specially-programmed computer, surfaces for each grid point in the 3D spatial grid, the surfaces in combination creating a plurality of grid cells; (d) defining, by use of the specially-programmed computer, an initial concentration of mass for each of the grid cells over the 3D spatial grid; (e) defining, by use of the specially-programmed computer, the velocity at each of the grid points in the 3D spatial grid by interpolating a pre-selected spatial 3D flow field to the 3D spatial grid; (f) calculating, by use of the specially-programmed computer, and using a first order upwind differencing scheme, fluid flow through each of the surfaces based on the velocities at each of the grid points; (g) computing, by use of the specially-programmed computer, a total flux through each of the surfaces based on the fluid flow; (h) computing, by use of the specially-programmed computer, a residual mass flux of layers of a water column based on the total flux and the residual mass flux of adjacent of the layers, the residual mass flux including residual velocities above a continuity threshold; (i) computing, by use of the specially-programmed computer, adjusted flow fields by removing the residual velocities from the velocities; (j) performing, by use of the specially-programmed computer, time-dependent advection/diffusion calculation to compute the concentration forecast based on the adjusted flow fields; (k) determining remaining of the residual velocities in the adjusted flow fields; (l) if the remaining residual velocities are above the continuity threshold, updating the spatial 3D flow field; and (m) repeating steps (e) through (l).