AbstractWater discharge and sediment flux variations are important parameters controlling the morphodynamic behaviour of rivers. Although quantitative estimates for water discharge and sediment flux variability are well‐constrained for modern rivers, far fewer assessments of flow and sediment flux intermittency in ancient fluvial systems from the rock record are available. In this study, a relationship between water discharge, sediment flux variability and patterns of changing fluvial stratigraphic architecture in the Middle Eocene Escanilla Formation, Spain, is explored. Water discharge intermittency factor (IWF), calculated as a ratio of the total water discharge (over the averaging time period) to the instantaneous channel‐forming water discharge if sustained for the same period, ranges from 0.03 to 0.11 in the high amalgamation intervals and from 0.10 to 0.32 in the low amalgamation intervals. Similarly, the sediment flux intermittency factor (ISF) is estimated to be in the range of 0.008 to 0.01 in the high amalgamation intervals and of 0.01 to 0.03 in the low amalgamation intervals. Consequently, high amalgamation intervals were most probably deposited under more intermittent and short‐lived intense precipitation events while low amalgamation intervals were the result of less intermittent flows spread throughout the year. Overall, these estimates are consistent with values from modern ephemeral rivers typically found in arid to semi‐arid climate and is in agreement with available proxy data for the Middle Eocene climatic context of the studied alluvial system. This highlights an important connection between hydroclimate, river morphodynamics and landscape evolution, and has implications to predict river flow and sediment transport across the Earth's surface in the geological past.