Water holes characteristic of the middle sections of fragmented, lowland, semi-arid rivers act as refuge areas for biota during low flow and drought. However, river regulation and catchment development has altered the hydrological and nutrient status of these refuges. A series of artificial ponds were used to imitate these habitats and experiments were designed to determine whether stochastically fluctuating water levels with maximum amplitude of 65cm would counteract the influence of nutrient enrichment on the growth of three key aquatic plant species. The species (Cyperus gymnocaulos, Triglochin procerum and Typha domingensis) represented different functional groups that inhabit contrasting zones across the elevation gradient. Each species was grown at a different elevation within the experiment reflecting each species' elevation preference and supplied with the equivalent to 0, 10 or 30gNm-2year-1. Under a static water regime nutrient enrichment doubled the total biomass of all three species. In contrast under a fluctuating water regime, nutrient addition did not influence total biomass of either T. domingensis or T. procerum and the performance of C. gymnocaulos was reduced by ca. 30%. These data suggest that if environmental flows were managed to provide a natural stochastically fluctuating water regime, this would nullify the influence of nutrient enrichment and limit the distribution and spread of invasive species such as Typha, that exists under the current altered conditions. Copyright (C) 2010 John Wiley & Sons, Ltd.