The surface of the ocean is very 'bumpy' comprising a very large range of phenomena which arise from wave processes and as a result of variations in the steric height (the specific volume) of the ocean waters. The kind of waves and steric height variations that are modelled by a general circulation model, like that used by BLUElink, are those affected by the earth's rotation and changes in water density at depth.

Familiar waves, like sea-swell and breaking waves, are too short to be influenced by the earth's rotation. The influence of tides on the ocean's general circulation is largely limited to mixing near the bottom in shallow water, such as shelves and reefs. Specialised models are already used by the Bureau to produce forecasts of these wave types.

A phenomenon that has a dominant influence on the general circulation of the ocean is the so-called 'eddy'. This term refers to a cyclonic motion (in the form of a vortex) on the scale 10 to 200 km in diameter that forms, propagates throughout the ocean and later decays. Throughout this cycle the eddies redistribute heat and salt. Common forms of eddies found in the Australian region are 'warm-core' and 'cold-core' eddies. These terms describe how the interior of the eddy is either warmer or colder than the surrounding ocean. A warmer, less dense water column has a larger specific volume leading to an increase in surface height and pressure compared to the surrounding ocean. In the presence of the earth's rotation, this pressure gradient radiating out from the warm core of the eddy is 'geostrophically' balanced by vortical currents circulating around the core. The term 'geostrophic' refers to the situation where, for an observer on the earth's surface, the vortical currents (the circulating currents flowing around the eddy) induce an equal and opposite Coriolis force to balance the gradient in pressure. A warm-core eddy, which has a pressure gradient radiating out, leads to anticyclonic motion, which is anticlockwise in the southern hemisphere. A cold-core eddy has a pressure gradient force that is focused toward the core, which leads to cyclonic motion that is clockwise in the southern hemisphere. Good examples of these can be found in the Tasman Sea as part of the East Australian Current. BLUElink has been specifically designed to model eddy motion in the Australian region.

The change in density between the eddy core and the surrounding ocean can be detected as a change in the surface height of the ocean of the order of one metre. Observing the surface height changes of eddies in the presence of all the other wave motion on the sea surface has been one of the most remarkable scientific achievements of the past decade. This has been made possible through satellite altimetry which measures the height of the ocean to great precision (see Jason). The BLUElink system uses this information to infer the correct position of eddies, their geostrophic motion as well as their temperature and salinity structure below the surface.