Water has become a precious resource in many parts of the world and its informed management is essential to a successful balance between human and environmental needs. As part of achieving this balance environmental flows have received much attention, but little rigorous biological evaluation. However reliably investigating biological responses to find causal links to E-flows has proven to be a challenge. The monitoring of larval fish abundance over eight years in the lower River Murray under a broad range of flow scenarios, including the Millennium drought, natural flood and within channel flows with delivery of E-flows, provides reliable information that associate E-flows to the presence of larvae of flow-cued spawning native fish. Our results show that the delivery of a flow pulse of appropriate magnitude and timing can prolong the period of time over which larvae of flow-cued spawning species are found in the lower River Murray. The temporal extension of early life history stages in the water column increases total abundance of larvae and potentially recruitment success. The results also highlight greater abundances of larvae in the gorge than floodplain geomorphic region of the lower River Murray, indicating the need for large spatial scales in the monitoring of E-flows. Identifying causal links of the observed patterns and relating them to ecological processes and function is essential for E-flow management in the lower River Murray and merits future research.