Hydrological extremes of unusually high or low river discharge may deeply affect the biogeochemistry of coastal lagoons, but the effects are poorly explored. In this study, microbial nitrogen processes were analyzed through intact core incubations and N-15-isotope addition at three sites in the eutrophic Sacca di Goro lagoon (Northern Adriatic Sea) both under high discharge (spring) and after prolonged low discharge (late-summer) of the main freshwater inputs. Under high discharge/nitrate load, denitrification was the leading process and there was no internal recycling. The site located at the mouth of the main freshwater input and characterized by low salinity exhibited the highest denitrification rate (up to 1150 +/- 81 mu mol N m(-2) h(-1)), mostly sustained by nitrification stimulated by burrowing macrofauna. In contrast, we recorded high internal recycling under low discharge, when denitrification dropped at all sites due to low nitrate concentrations, reduced bioturbation and nitrification. The highest recycling was measured at the sites close to the sea entrance and characterized by high salinity and particularly at the clams cultivated area (up to 1003 +/- 70 mu mol N m(-2) h(-1)). At this site, internal recycling was sustained by ammonification of biodeposits, bivalve excretion and dissimilatory nitrate reduction to ammonium (DNRA), which represented 30% of nitrate reduction. Flash floods and high nitrate loads may overwhelm the denitrification capacity of the lagoon due to the reduced residence time and to the saturation of microbial enzymatic activity, resulting in high transport of nitrate to the sea. Prolonged dry periods favor large internal recycling, due to a combination of high temperatures, low oxygen solubility and low bioturbation, which may prolong the extent of algal blooms with negative effects on lagoon biogeochemical services. We condude that hydrological extremes, which are expected to become more frequent under climate change scenarios, strongly alter N cycling in coastal sediments.