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This study attempts to describe changes in plankton biomass (including bacteria, phytoplankton, ciliates, rotifers, and crustaceans) in the semi-arid, hypertrophic, freshwater wetland, Las Tablas de Daimiel National Park (central Spain), in relation to water inflow. An inter-annual comparison of 1996 and 1997, with contrasting rainfall, reveals that inflows in the form of flooding act as a bottom-up structuring force on total plankton biomass. However, the responses of plankton biomass to flooding were different in strength between the two years, which can be attributed to shifts in plankton community structure. Crustacean zooplankton conditioned total plankton biomass in 1996, based on the relationship between the high individual biomass and community development. Crustaceans decreased in 1997, while bacteria, phytoplankton and rotifers increased. The quantitative increase of the latter groups resulted in a higher total plankton biomass in 1997. The key position of crustaceans in the wetland plankton is also reflected in their capability for exerting significant top-down control, which was clearly evident in 1996 but weaker in 1997, based on their numerical reduction. Statistical analyses provide evidence that the decline of trophic interactions in 1997 is related to the strength of flooding in that year, thereby highlighting the significance of the disruptive action of physical disturbance on biotic interactions in the plankton. Flooding and areal inundation were also shown to be significant for spatial heterogeneity. In 1996, site-specific development took place in the absence of prolonged flooding effects, resulting in high spatial heterogeneity. In 1997, however, remarkable homogenization of plankton biomass occurred along the major water flow path. Thus, wetland landscape heterogeneity depends on inflows which condition areal inundation. This, in turn, influences plankton dynamics.