Liverpool Bay is a region of freshwater influence which receives significant freshwater loading from a number of major English and Welsh rivers. Strong tidal current flow interacts with a persistent freshwater-induced horizontal density gradient to produce strain-induced periodic stratification (SIPS). Recent work (Palmer in Ocean Dyn 60:219–226, 2010; Verspecht et al. in Geophys Res Lett 37:L18602, 2010) has identified significant modification to tidal ellipses in Liverpool Bay during stratification due to an associated reduction in pycnocline eddy viscosity. Palmer (Ocean Dyn 60:219–226, 2010) identified that this modification results in asymmetry in flow in the upper and lower layers capable of permanently transporting freshwater away from the Welsh coastline via a SIPS pumping mechanism. Observational data from a new set of observations from the Irish Sea Observatory site B confirm these results; the measured residual flow is 4.0 cm s−1 to the north in the surface mixed layer and 2.4 cm s−1 to the south in the bottom mixed layer. A realistically forced 3D hydrodynamic ocean model POLCOMS succeeds in reproducing many of the characteristics of flow and vertical density structure at site B and is used to estimate the transport of water through a transect WT that runs parallel with the Welsh coast. Model results show that SIPS is the dominant steady state, occurring for 78.2% of the time whilst enduring stratification exists only 21.0% of the year and enduring mixed periods, <1%. SIPS produces a persistent offshore flow of freshened surface water throughout the year. The estimated net flux of water in the surface mixed layer is 327 km3 year −1, of which 281 km3 year−1 is attributable to SIPS periods. Whilst the freshwater component of this flux is small, the net flux of freshwater through WT during SIPS is significant, the model estimates 1.69 km3 year−1 of freshwater to be transported away from the coast attributable to SIPS periods equivalent to 23% of annual average river flow from the four catchment areas feeding Liverpool Bay. The results show SIPS pumping to be an important process in determining the fate of freshwater and associated loads entering Liverpool Bay.