In tide-dominated environments, residual circulation is the comparatively weak net flow in addition to the oscillatory tidal current. Understanding the 3D structure of this circulation is of importance for coastal management as it impacts the net (longer term and event-scale) transport of suspended particles and the advection of tracer quantities. The Dee Estuary, northwest Britain, is used to understand which physical processes have an important contribution to the time-varying residual circulation. Model simulations are used to extract the time-varying contributions of tidal, riverine (baroclinicity and discharge), meteorological, external and wave processes, along with their interactions. Under hypertidal conditions, strong semi-diurnal interaction within the residual makes it difficult to clearly see the effect of a process without filtering. An approach to separate the residual into the isolated process contribution and the contribution due to interaction is described. Applying this method to two hypertidal estuarine channels, one tide dominant and one baroclinic dominant, reveals that process interaction can be as important as the sub-tidal residual process contributions themselves. The time variation of the residual circulation highlights the impact of different physical process components at the event scale of tidal conditions (neap and spring cycles) and offshore storms (wind, wave and surge influence). This gives insight into short-term deviation from the typical estuarine residual. Both channels are found to react differently to the same local conditions, with different short-term change in process dominance during events of high and low energy.