IntroductionSeagrass meadows worldwide are in decline due to cumulative stressors that degrade water quality and habitat conditions, exacerbated by ongoing climate change, prompting increasing interest in restoration as a management response.MethodsHere, we interwove Indigenous knowledge, habitat suitability modelling, and a field‑based restoration trial to evaluate the feasibility of restoring Nanozostera muelleri in Waihī Estuary, New Zealand.ResultsEnvironmental assessments indicated that the selected restoration sites met commonly reported thresholds for seagrass growth, with adequate light availability and favourable sediment organic matter and mud content. Habitat suitability modelling further identified these locations as areas of high restoration potential. However, despite selecting sites predicted to support seagrass, transplant performance declined consistently regardless the use of three transplantation methods. Seagrass cover, shoot density, and leaf length decreased significantly from initial planting through the six monitoring times, indicating that acute stressors (e.g., episodic freshwater inputs, energetic hydrodynamics, and potentially unmeasured biogeochemical or biological pressures) limited early establishment.DiscussionOur findings highlight a clear mismatch between broad‑scale habitat suitability and fine‑scale environmental conditions that determine transplant success. Our study highlights the need for multi‑scale, evidence‑based restoration planning that couples site‑level interventions with reductions in catchment‑derived nutrient and sediment inputs, without which long‑term recovery is unlikely. By combining Indigenous knowledge, spatial modelling, and empirical trials, this work provides a framework for improving seagrass restoration outcomes in degraded estuarine ecosystems and advancing collaborative, land-to-sea approaches to coastal habitat recovery.