Context Globally, intermittently closed and open lakes and lagoons (ICOLLs) can constitute highly productive coastal environments that support a range of fisheries. With growing pressures on fish communities, understanding the role of ICOLL management in population dynamics is increasingly important for conservation. Aims To determine whether the flood-driven management and environmental degradation of New Zealand’s largest coastal lake, Te Waihora–Lake Ellesmere, has created a conflict with the life history of diadromous īnanga, Galaxias maculatus Jenyns, potentially limiting persistence of this species. Methods The timing of post-larval migration of īnanga was assessed over 2 years (2021 and 2022) and compared with historic patterns of managed lake openings. Immigrating īnanga individuals were tagged to assess subsequent development, before potential reproductive output was quantified using artificial spawning substrates. Key results Peak migration periods were mismatched with the timing of most lake openings. After quickly transiting into tributaries, īnanga seemingly died within a few months. No spawning was detected. Conclusions and implications The mismatch between lake opening management and the annual life history of īnanga prevents the reliable supply of post-larvae needed to sustain a persistent population, with severe environmental degradation being likely to restrict subsequent survival through summer conditions. This study has highlighted the need for management interventions to be tuned to the life histories of at-risk species.