Seagrasses are true plants that live in shallow marine water of both tropical and temperate waters. Seagrass meadows are crucial for primary production and biodiversity, carbon sequestration, water purification, coastal protection and food for megafauna like dugongs. This chapter combines desk work (systematic review of existing publications) and field assessment, highlighting multiple impacts of cyclones and floods on seagrass. SPOT 5 and Landsat imagery were used for mapping over 21-year period (1992–2013), and changes in Inhambane Bay are linked to multiple cyclones that prompted a total seagrass area reducing from 12,076 ha to 6199 ha (51% of the original area). In Maputo Bay, seagrasses were impacted by both the 2000 floods and anthropogenically due to poor practices of uprooting seagrasses for clam collection. Seagrasses reduced 7% a year in western Maputo Bay and 1.2% in Inhambane Bay. The study also documents impact of extreme events on the catches of a sardine, Amblygaster sirm, in Inhambane Bay and on clams abundance and species diversity in Maputo Bay. The construction of new wave breakers in Maputo city prompted land reclamation and may have led to the disappearance of bivalves Salmacoma litoralis and Anadara antiquata. This account on seagrass status formed the basis for seagrass restoration initiative.