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Archimer http://archimer.ifremer.fr Highlights ► Flash flood discharges were 8% and 3% of the yearly averaged total nitrogen and phosphorus loads. ► Substantial increase of labile trace metals in lagoon waters was not mainly due to river loads. ► Bacterial production was limited by the reduction in DOC availability during the flood event. ► DIN enrichments was beneficial for the production of the most resilient lagoon phytoplankton. ► The enhanced microbial production was mainly filtered or exported through sedimentation.