The Macquarie Marshes is an intermittently flooded wetland complex covering nearly 200,000. ha. It is one of the largest semi-permanent wetland systems in the Murray-Darling Basin, Australia, and portions of the Marshes are listed as internationally important under the Ramsar Convention. Previous studies indicate that the Marshes have undergone accelerated ecological degradation since the 1980s. The ecological degradation is documented in declining biodiversity, encroaching of terrestrial species, colonisation of exotic species, and deterioration of floodplain forests. There is strong evidence that reduction in river flows is the principal cause of the decrease in ecological values. Although the streams are relatively well gauged and modelled, the lack of hydrological records within the Marshes hampers any attempts to quantitatively investigate the relationship between hydrological variation and ecosystem integrity.To enable a better understanding of the long-term hydrological variations within the key wetland systems, and in particular, to investigate the impacts of the different water management policies (e.g. environmental water) on wetlands, a river system model including the main wetland systems was needed. The morphological complex nature of the Marshes means that the approximation of hydrological regimes within wetlands using stream hydrographs would have been difficult and inaccurate. In this study, we built a coupled 1D/2D MIKE FLOOD floodplain hydrodynamic model based on a 1. m DEM derived from a LiDAR survey. Hydrological characteristics of key constituent wetlands such as the correlation between water level and inundation area, relationships between stream and wetlands and among wetlands were estimated using time series extracted from hydrodynamic simulations. These relationships were then introduced into the existing river hydrological model (IQQM) to represent the wetlands.The model was used in this study to simulate the daily behaviours of inflow/outflow, volume, and inundated area for key wetlands within the Marshes under natural conditions and recent water management practices for the period of July 1 1991 to June 30 2009. The results revealed that the recent water management practices have induced large changes to wetland hydrology. The most noticeable changes include the dramatic reductions in high flows (i.e. flows with less than 25% exceedence, reduction ranges from 85% to 98% of the high flow peak depending on the location), areal inundation extent (ranging from 13% to 79% depending on climatic conditions), and flow rising/falling rates (over 90% for high flows). Our analysis also highlighted that the impacts of water management practices on some of the flow variables for wetland habitats contrasted with those for instream habitats. For example, we did not find any evident alterations in the low flows (i.e. 75% exceedence) attributable to water management.