Understanding energy flow through ecosystems is vital for effective environmental management. Ecosystem processes controlling basal resource production and availability are determined by the physical properties of a system. In aquatic systems, the hydrological regime is the primary driver of those physical properties. Floodplain wetlands are by nature hydrologically variable, and exhibit physical properties across a dynamic patchwork of habitats which experience different hydrological regimes over long- and short- time frames. We investigated whether these patch types produce basal resources of differing nutritional quality, and how these patches interact through an inundation cycle. Using fatty acid analyses, we identified differences in basal resource quality between intermittently and permanently inundated patches and describe patterns in basal resource quality throughout an inundation cycle. Overall, basal resource quality was highest in intermittently inundated sites where a low, open vegetation structure supported higher algal production compared to permanently inundated sites with a tall, dense vegetation structure. Although site type was a significant factor in basal resource quality overall, inundation stage and the interaction between site type and stage proved powerful factors in determining the distribution of resources and both temporal and spatial subsidies appear important in this system. Our research indicates that hydrology influences basal resource quality, and provides a basis for further research to improve our understanding of how to maximise wetland productivity by managing hydrology for resource quality.