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The intensifying impacts of aridity and water stress on the dynamics and ecological degradation of wetlands in North Africa are often underestimated and largely remain unquantified. To address this deficiency, we assessed decadal changes in the sedimentary, sea surface salinity (SSS), and microfaunistic patterns of the Bizerte Lagoon, a climatically vulnerable area in the southern Mediterranean basin. Findings from sediment transport analysis indicate preferential current dispersion along the lagoon ridge associated with mixtures of sedimentary distributions. The changes in SSS between 2004 and 2016 reveal an increase of approximately 40% in areas where the river flows into the lagoon. Findings from the microfaunistic analysis suggest that over the last few decades, a progressive enrichment of alien marine species has occurred in the lagoon owing to changes in SSS and sedimentation. Results also revealed the unexpected presence of tropical to subtropical Larger B-bearing Foraminifera (LBF) species, which are exogenic to the warm southern Mediterranean coasts. The study findings highlight the impacts of damming and changes in precipitation patterns on the degradation of biodiversity in the Bizerte Lagoon and in other lagoonal systems in North Africa with similar levels of aridity.