Public Natural Resource Management (NRM) agencies operate in complex social-ecological domains. These complexities proliferate unpredictably therefore investigating and supporting the ability of public agencies to respond effectively is increasingly important. However, understanding how public NRM agencies innovate and restructure to negotiate the range of particular complexities they face is an under researched field. One particular conceptualisation of the social-ecological complexities facing NRM agencies that is of growing influence is the Water–Energy–Food (WEF) nexus. Yet, as a tool to frame and understand those complexities it has limitations. Specifically, it overlooks how NRMs respond institutionally to these social-ecological complexities in the context of economic and organisational challenges—thus creating a gap in the literature. Current debates in public administration can be brought to bear here. Using an organisational cultures approach, this paper reports on a case study with a national NRM agency to investigate how they are attempting to transform institutionally to respond to complexity in challenging times. The research involved 12 elite interviews with senior leaders from Natural Resources Wales, (NRW) and investigated how cultural narratives are being explicitly and implicitly constructed and mobilised to this end. The research identified four distinct and sequential cultural narratives: collaboration, communication, trust, and empowerment where each narrative supported the delivery of different dimensions of NRW’s social-ecological complexity mandate. Counter to the current managerialist approaches in public administration, these results suggest that the empowerment of expert bureaucrats is important in responding effectively to complexity.