Salt marshes are vital coastal ecosystems, increasingly threatened by rising sea level and human pressures, that provide essential services, including coastal protection, habitat support, and carbon sequestration. This study examines the effectiveness of different eco-engineering structures in restoring salt marshes in the Mondego Estuary, Portugal, by assessing their impacts on benthic macroinvertebrate communities as bioindicators of ecosystem health. The experimental design included five experimental cells: wood palisade (Fence), geotextile fabric (Geotextile), geotextile bags filled with sand (Bags), a cell with autochthonous vegetation (Plants), and a Control cell with bare soil. Monitoring took place from 2019 to 2021, with both before and after intervention sampling to evaluate species composition, biomass, and density. Key ecological indices, such as the AZTI’s Marine Biotic Index (AMBI), Shannon-Wiener Diversity, and Pielou’s Evenness, were calculated alongside measurements of environmental variables. The results indicated minimal impacts on biodiversity, with observed variations primarily attributed to seasonal dynamics. While the wood palisade enhanced species richness and density, geotextile provided better community stability. The findings emphasize the importance of long-term monitoring, stakeholder engagement, and sustainable use of materials to optimize restoration efforts and better inform coastal management strategies in the face of climate change.