Proxy data suggest that atmospheric CO2 levels during the middle of the Pliocene epoch (about 3ĝ€‰Myr ago) were similar to today, leading to the use of this interval as a potential analogue for future climate change. Estimates for mid-Pliocene sea levels range from 10 to 40'm above present, and a value of +25'm is often adopted in numerical climate model simulations. A eustatic change of such magnitude implies the complete deglaciation of the West Antarctic and Greenland ice sheets, and significant loss of mass in the East Antarctic ice sheet. However, the effects of glacial isostatic adjustments have not been accounted for in Pliocene sea-level reconstructions. Here we numerically model these effects on Pliocene shoreline features using a gravitationally self-consistent treatment of post-glacial sea-level change. We find that the predicted modern elevation of Pliocene shoreline features can deviate significantly from the eustatic signal, even in the absence of subsequent tectonically-driven movements of the Earth's surface. In our simulations, this non-eustatic sea-level change, at individual locations, is caused primarily by residual isostatic adjustments associated with late Pleistocene glaciation. We conclude that a combination of model results and field observations can help to better constrain sea level in the past, and hence lend insight into the stability of ice sheets under varying climate conditions.