SPATIAL DISCRETIZATION in MT3D is the same as MODFLOW

x, y, z coordinates are:

0,0,0 in upper top left corner of row 1 col 1 layer 1

(z is positive downward)

MT3D does not have limits on grid size, however

mass balance errors can grow large if cell sizes are too large

discretization may be too coarse, impacting interpolation and averaging the dispersive step over large distances

One rule for limiting cell size is to strive for a reasonable Peclet number
TEMPORAL DISCRETIZATION in MT3D begins the same as the MODFLOW simulation

MT3D and MODFLOW will have the same number of stress periods, unless MODFLOW is a steady state model, in which case it will have one stress period and MT3D may have many

time steps used for head may be too large for transport

transport step length can be specified,
but if it is too large MT3D's automatic step size control takes over