In the conventional approach to geophysical fluid dynamics, only the horizontal components of the Coriolis force due to horizontal motions of the fluid are taken into account. All the other components of the Coriolis force, which are called the non-traditional (NT) terms, are considered to be small second order quantities and are usually dropped. This effectively simplifies the system and the nice and clean quasi-geostrophic (QG) equation can be obtained, which is widely used in analytical studies of climate systems. Interest has been drawn to the dropped terms in recent studies. It is shown that in some special cases these second order terms actually have a noticeable influence on the dynamics of the system. However, a full picture of these terms in the dynamics of the real ocean is still lacking. Here, we will start from the fundamental equations of fluid dynamics, and through careful scaling analysis conduct a detailed study of the governing equations of geophysical fluid dynamics while keeping the NT terms. We will specifically investigate the influence of these NT terms on equatorial waves, since near the equator the NT components of the Coriolis force are the most significant. / text