Coastal wetlands are highly sensitive to changes occurring at the coastline. It is critically important to determine region-specific projections for these areas due to their specificities and vulnerabilities to climate change. This work aimed to value the impacts of recent climate changes at West Africa Sahara coastland, southern Morocco, at Khnifiss Lagoon. We have applied a combined approach using remote sensing techniques and environmental reconstructions based on high-resolution analysis of sediment cores, covering the current warm period. Remote sensing highlighted changes to the lagoon inlet, accompanied by a greater meandering character of the tidal channels. As a response, the sediment cores have recorded a predominant vegetation substitution due to changes in the tidal limit, and an increase in organic carbon accumulation was observed. For the current climatology, during positive phases of the North Atlantic Oscillation, winds reaching the coast strengthen in an east-to-west direction. In the Khnifiss Lagoon, whose inlet is dominated by the ebb tide, the intensity and direction of the winds on the coast at surface level modifies its connection to the ocean by increasing sediment transport toward the interior of the lagoon. Locally biological responses to wind intensification, and possibly sea-level rise, exemplify the lagoon sensitivity to large-scale processes. Coastal vegetated wetlands are considered to be highly dynamic environments. However, we expect a loss of the upper tidal vegetation due to boundary conditions limiting the accommodation space in this arid environment in a possible future scenario of continuously inland tidal line displacement.