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Ephemeral wetlands are an important part of many arid ecosystems, providing stepping stones for migratory bird movements, opportunistic feeding and breeding resources when flooded, and potentially also important drought refuge for resident bird populations. However, ephemeral wetlands are extremely challenging to monitor, due to their dynamic nature and access issues. The Fortescue Marsh (Martuyitha) is one of the largest water features of northwest Australia, with significant cultural and ecological value. Understanding hydrological drivers influencing waterbird counts and diversity at this ephemeral wetland are vital towards building a baseline for comparison of future monitoring. We compared results of 9 ground-based and 13 aerial waterbird population surveys carried out over the last 40 years with remote-sensed measures of flood area over preceding months. Generalised linear modelling indicated strongest influence of flood extent and duration of flooding, with peak counts and species richness around 5–8 months following extensive floods. There was also an effect of survey method, with greater counts and species richness recorded by aerial rather than ground surveys; differences in bird community recorded are likely due to conflation of flood extent and survey method. Fluctuations in survey results over time reflect the stochastic nature of flooding in this arid landscape, where rainfall and streamflow are a direct result of cyclonic activity. Results of this study identify a modelling approach that will allow robust monitoring that can adapt to variability in both survey method and timing.