Over half of the total nitrogen, phosphorus, silicate and dissolved organic carbon (DOC) loading was discharged from the Wile River into the Thau Lagoon waters within the first five days of what was considered to be the autumn flash flood period. Such loads represented about 8% and 3% of the yearly averaged total nitrogen and phosphorus load in Thau Lagoon, respectively. Although this event affected >20% of the total lagoon volume, river trace metal loads contributed apparently only weakly to the increase in labile trace metal concentrations in the lagoon surface waters. Differences between theoretical dilution values and observed values were also noticed for phosphate, silicate and dissolved organic carbon (DOC) concentrations. DOC losses (10-50%) mainly through flocculation, together with the substantial increases in some metallic contaminants such as Zn (from 6 to >30 mu g L-1) observed during the flash flood in saline lagoon waters, may have limited the carbon production of bacterial communities. The potential osmotic shock and the increase in turbidity may mainly explain the low phytoplankton C turnover rates (average of 0.02 h(-1)) measured in brackish waters (<30) during periods of heavy flood discharge. The dissolved inorganic nitrogen (DIN: NO3 + NH4) enrichment measured 12 days after the flash flood event in saline lagoon surface waters (from 22 to 143 mu g N L-1) led to a substantial increase in phytoplanktonic C production and associated DIN uptake rates (from 2.6 to 7.0 mu g C L-1 h(-1) and from 0.5 to 1.1 mu g N L-1 h(-1), respectively). Subsequent accumulation in particulate organic carbon and nitrogen was not observed in the area studied during and after the flash flood period, averaging 549 +/- 50 mu g C L-1 and 168 +/- 9 mu g N L-1, respectively. This suggests that most of locally produced microbial production was rapidly filtered by oysters contributing to about 13% of the yearly exploited production in the lagoon and/or exported through sedimentation. (C) 2012 Elsevier Ltd. All rights reserved.