This paper presents a study of two transport timescales (TTS), i.e., the residence time and exposure time, of a hyper-tidal estuary using a widely used numerical model. The numerical model was calibrated against field measured data for various tidal conditions. The model simulated current speeds and directions generally agreed well with the field data. The model was then further developed and applied to study the two transport timescales, namely the exposure time and residence time for the hyper-tidal Severn Estuary. The numerical model predictions showed that the inflow from the River Severn under high flow conditions reduced the residence and exposure times by 1.5 to 3.5% for different tidal ranges and tracer release times. For spring tide conditions, releasing a tracer at high water reduced the residence time and exposure time by 49.0% and 11.9%, respectively, compared to releasing the tracer at low water. For neap tide conditions, releasing at high water reduced the residence time and exposure time by 31.6% and 8.0%, respectively, compared to releasing the tracer at low water level. The return coefficient was found to be vary between 0.75 and 0.88 for the different tidal conditions, which indicates that the returning water effects for different tidal ranges and release times are all relatively high. For all flow and tide conditions, the exposure times were significantly greater than the residence times, which demonstrated that there was a high possibility for water and/or pollutants to re-enter the Severn Estuary after leaving it on an ebb tide. The fractions of water and/or pollutants re-entering the estuary for spring and neap tide conditions were found to be very high, giving 0.75–0.81 for neap tides, and 0.79–0.88 for spring tides. For both the spring and neap tides, the residence and exposure times were lower for high water level release. Spring tide conditions gave significantly lower residence and exposure times. The spatial distribution of exposure and residence times showed that the flow from the River Severn only had a local effect on the upstream part of the estuary, for both the residence and exposure time.