One of the common techniques used in application of time-dependent, three-dimensional models addressing estuarine and coastal environmental problems is the sigma coordinate transformation. This transformation has proven useful in applications with highly irregular bottom topography. However, numerous modeling studies have noted difficulties, including spurious density-induced motions and increased velocity fields at depth in variable topography domains. Calculations are presented to illustrate that the common practice of neglecting terms proportional to deltah/deltax and deltah/deltay in the transformed equations can be responsible for spurious velocities.