It is common for surface water-groundwater interaction assessments to investigate river reaches at a local scale and as discrete individual systems, which are generally classified as connected (gaining and losing type systems) or disconnected (transitional or completely disconnected type systems). While these classifications are valid at any point in space and time, studies often fail to consider how individual river reaches function in the context of the entire regional river system (comprising multiple river reaches) and what implications this can have on water quantity and quality. In this study, spatial and temporal assessments were made in a regional catchment using hydraulic, hydrochemical, and tracer-based techniques to determine the source and loss terms of the river and groundwater system and how their relative magnitude changes along the river from the catchment headwaters towards the sea. Applying an entire regional river system assessment we demonstrate that the state of connection can change along river reaches, as well as take place concurrently at the same location. Water level data, together with salinity and stable isotope results showed that the relatively low salinity of the fresh water river system was maintained in an otherwise saline regional groundwater system by virtue of the lack of saline groundwater inputs in a river with a dominantly losing connectivity state. This losing state was strongly influenced by the high evapotranspiration of the native vegetation. By determining the state of connection between surface water and groundwater and understanding the variable and complex nature of contiguous river reaches of an entire regional river system more appropriate management practices can be employed.