Freshwater ecosystems are both incredibly biodiverse and highly threatened globally.Variation in environmental parameters including habitat and flow can substantially affect many ecological processes within riverine aquatic communities, but the ties between such parameters and ecology are neither well studied nor understood. In highly variable tropical dryland river systems, assessing such relationships requires data collection over inter-decadal time scales, which is not typically permitted on development schedules driven over short periods (including election and funding cycles).Here, we used seine net sampling data collected over an 18-year period in the tropical dryland Fitzroy River, Western Australia, to assess how environmental and temporal factors including habitat, seasonality, and inter-annual variation in wet season magnitude affect the community assemblage structure, recruitment, and growth of aquatic species in dryland rivers. Results demonstrated that macrohabitat (main channel vs floodplain creek) and the magnitude of wet season rains and resultant flooding both had a substantial influence on biotic communities, alongside seasonal and diel variation. The magnitude of wet season flooding (measured as river discharge volume) had the greatest impact on assemblage composition within floodplain creek habitats and was a significant driver of recruitment rates and growth of recruits and adults of several species examined. This study highlights key considerations for conserving dryland river systems and constituent biota. Specifically, these are maintaining (a) rhythmicity of flow within each year, (b) diversity of flow volume between years, and (c) a variety of habitat types including ephemeral, semi-permanent, and permanent shallow floodplain and deeper main channel pools, in order to support a diverse array of generalist and specialist diadromous and potamodromous fishes.