Abstract Wetland hydro-ecology is a key research field for ecologists, hydrologists and wetland investigators to quantify the relationship between wetland ecological patterns and hydrological mechanisms. Existence and functioning of wetlands is crucial for adjacent terrestrial and aquatic ecosystems. Hydro-ecological research promotes both protection and restoration of healthy natural wetlands by further understanding the biophysical characteristics of wetland habitats. This study establishes a wetland hydro-ecological model with the methodological support from geographic information system (GIS) and remote sensing (RS). It conceptualises a cause–effect chain interface from the real wetland ecosystem. GIS and computer modelling methods are used to generate the hydrological indicators based on a Digital Elevation Model (DEM). By interpreting multi-temporal RS images, we produce wetland classification information and various landscape indices. Both hydrological and landscape indicators are used to integrate the hydro-ecological analysis with some multidisciplinary analysis methods. For the application of the wetland hydro-ecological model, we present a case study in an inland floodplain wetland within the scale of a catchment. The study site is the Honghe National Nature Reserve (HNNR), a Ramsar-designated site on the Sanjiang Plain in Northeast China. The multi-temporal Landsat TM 7 images and a DEM of the study area at finer scale are used to generate the various indicators of the wetland biophysical habitats. Field monitoring data of hydrology and ecology are used to calibrate the generated digital information. Our hydro-ecological analysis presents two significant results by coupling the wetland landscape ecology into hydrological units: (1) the constitutions of the wetland communities (an ensemble of plants that are specially equipped to live in soggy conditions) in the riverine or non-riverine biophysical habitats are clearly different in HNNR. The patch area and numbers of wetland communities increased from the forestry communities, the bush communities, the meadow communities through to the marshes in a good moisture gradient within the riverine zone, while the predominant patch area and number replaced by the transitional meadow communities beyond the riverine zone; (2) the flood water plays a key role on controlling the distribution of the wetland communities in HNNR. The predominant distribution of typical marsh communities in the yearly saturated zone exchanged into the larger distribution of the wet meadow in the seasonal saturated zone, and then finally replaced by the predominant distribution of the wet meadow in the yearly unsaturated zone. Furthermore, a cluster analysis for quantitative spatial characteristics of wetland distribution shows the numerical difference between marshes and non-marshes biophysical habitats in the core HNNR.