The Ter Vell (NE Iberian Peninsula) is a eutrophic coastal lagoon which has been flooded by the excess irrigation water and the agricultural runoff during the last decades. Between 1999 and 2003, restoration measures were applied to improve its water quality. At the same time, but independently, agricultural water management drastically reduced the freshwater inflow. The short-term effects of these management actions on the limnological characteristics of the lagoon were analysed by comparing two hydrological cycles, one before (1999/2000) and the other one after (2002/2003) the actions. The two cycles are illustrative of opposite situations in the hydrological functioning of coastal wetlands. In the first, the lagoon was exorheic, with prolonged flooding periods and a low residence time; in the second, it had a more endorheic character, with scarce water inputs and prolonged periods of confinement. Consequently, nitrogen inputs diminished and organic load and salinity increased as the internal loading and the accumulation effects became more relevant. These effects were actually caused by the drastic reduction in the freshwater inflow which prevented, in turn, the success of the restoration measures. The zooplankton community of the Ter Vell lagoon was not significantly altered by the hydrological change, at least in the short-term, and rotifers and cladocerans, mainly those species indicative of eutrophy, dominated the community.