This study analyzes the management alternatives that are currently considered by public administrations in the Guadalquivir River Estuary, which is a well-mixed and rather channelized estuary in the southwest of Spain. A linearized multichannel exploratory model that operates at tidal and averaged scales is used. The model extends the previous developments for calculating the tidal variations of salinity and provides elevations, currents and salinity. The effects of the change in mean depth of the main navigation channel, the reconnection of a secondary tidal channel (Brazo del Oeste) and the recovery of a marsh in the lower part of the estuary are the three alternatives analyzed. The model outputs indicate that the channel deepening would produce an increase in the amplitudes of the elevations, tidal salinities, and tidal prisms, as well as the extent of the saline intrusion. Similar effects could be alternatively obtained with the reconnection of the secondary channel with suitable design parameters. The increase in tidal elevations due to channel deepening should therefore be considered in any dredging project, because lower sediment volumes need to be dredged to attain the projected water column height at high water. The recovery of marshes notably influences the tidal wave propagation when the connecting width with the navigation channel exceeds one hundred meters. Its most remarkable effect is to increase the tidal amplitudes and to reduce the tidal currents upstream the connection point in proportion to the degree of connectivity with the main channel. A combination of alternatives could potentially serve to mitigate the specific effects of individual alternatives. The effects of channel deepening on the amplitudes of the tidal elevation and the currents could be partially compensated for through the recovery of tidal marshes.