The Tagus Estuary is one of the largest in Europe with 320 km2, and it has been, for centuries, a gateway to Lisbon. This study focuses on the Moita-Montijo Bay and on the recent dynamics of its tidal flats and saltmarshes. Aerial photographs, orthomosaics, and very high-resolution satellite imagery were used to analyze landcover and shoreline changes. Tidal flats have shown expansion from 1977 to 1995, but since then, contraction dominated, with a change of position of the tidal flat edge of −2.8 m/year in the north bank and −4.2 m/year in the south bank of the Montijo channel. Most contraction occurred along the route of the fast transport catamarans that started operating in 1995, while in the sector without catamaran navigation, expansion was observed. Saltmarshes have been suffering contraction since 1958, with increased rates after 1995 (−0.38 to −0.44 m/year), especially along the catamaran route (−0.57 to −1.27 m/year). The analysis of the wake generated by different vessel types shows a wake increase with the catamarans, in agreement with the increase in contraction along the Montijo channel. Inside abandoned salt pans, saltmarshes expanded. Since 1995, major changes are also observed along the tidal flat margin, with the formation of coarse lag deposits of coarse sands and shells. Given the contraction increase associated with catamaran traffic and the resulting degradation of the tidal flat and the saltmarshes, it is important to introduce measures for containing contraction.