The ecological communities supported by freshwater habitats and wetlands that persist from floodplain inundation generate numerous cultural, recreational and economic values via commercial fisheries and other human uses of these habitats. However, the alteration of flow connectivity, degradation, and disruption of physical processes that sustain different levels of organisms (e.g., primary producers) are threats that affect aquatic biodiversity and the productivity of these habitats. Therefore, the large scale assessment of freshwater habitats for proactive water resources planning and the development of climate change mitigation and resource management strategies is essential. However, such monitoring and assessment is complicated by the inaccessibility of many large wetland systems during times of inundation, making in situ sampling unfeasible at a time when high levels of aquatic primary producers are generating food and energy sources for higher order consumers. To understand the physical dynamics of aquatic primary producers and freshwater habitats (1991–2019) during such times in a large floodplain river in northern Australia (Gilbert catchment), this study integrated Landsat-derived modified normalised difference water index and normalised difference vegetation index in a classification tree model. Thereafter, key hydrological drivers (rainfall and river discharge) of floodplain productivity and connectivity were assessed using a range of multivariate techniques. Results show that the floodplain had a high aquatic plant biomass during the summer wet season based on the correlation between aquatic biomass accumulation (hot spots) and inundation ( @ phase lag < 1 month) during such period. River discharge ( @ lag = 1 month) at downstream Gilbert catchment appear to be a relatively stronger indicator of hot spots of floodplain biomass accumulation as opposed to local rainfall ( @ lag = 3 months). While the downstream discharge explains a significant proportion of variability in the leading orthogonal mode of rainfall (), statistical relationships developed between discharge/rainfall and the distribution of aquatic primary producers confirm that both rivers (flow) and local rainfall are key optimal predictors of inundation and sites of primary producers with river flows being a better indicator of the latter. It is therefore argued that hydro-meteorological fluctuations will be key constraints on freshwater habitats and the growth of primary producers, albeit, human disturbance of flow can impact on floodplain productivity. As illustrated in this study, such constraints are reflected in the spatial patterns and changing characteristics (connectivity and spatial heterogeneity) of hot spots of primary producers and freshwater habitats (Palustrine, Lacustrine, and Riverine ecosystems).