The Guadalquivir estuary (SW, Spain) is a complex system influenced by various factors such as maritime traffic, agricultural and aquaculture water usage, and its proximity to the UNESCO Biosphere Reserve, Doñana. Recent attention has been given to the restoration of shores and marshes. The recovery of tidal flats in the lower estuary has long been proposed as a solution to shore degradation and potential negative impacts from bathymetric changes. However, previous studies have relied on basic 1D models, calling for more comprehensive investigations using advanced computational models like the one developed by GOFIMA. This study focuses on simulating tidal flats with different surfaces, depths, and locations connected to the navigation channel. Results are compared with a configuration excluding tidal flats, considering only the main force (astronomical tide) and fixed boundary conditions. The aim is to understand the effects of tidal flats recovery on tidal harmonics of surface oscillations and currents, and the salinity distribution along the estuary. Findings highlight the critical role of the amount of water exchanged with restored tidal flats and their location in inducing changes in tidal and saline dynamics. Future research will explore additional physical variables and realistic scenarios of tidal flat restoration.