Stormwater management has evolved beyond flood control to include ecosystem protection. Real-time control technology now enables adaptive systems that can maintain stream flows and habitat, but these require ecologically-relevant flow objectives based on habitat requirements. We developed a five-step method for integrating flow-habitat relationships into stormwater control: defining habitat requirements, conducting high-resolution surveys, hydrodynamic modelling, creating flow-habitat curves, and embedding these into control algorithms. We applied this to the Monbulk Creek Smart Water network which aims to protect vulnerable platypus populations. We identified four key habitat metrics for platypus (wetted area, swimmable depth, pool habitat, large wood). Then, flow-habitat curves based on feature survey and 2D TUFLOW modelling across eight reaches were developed to show how habitat availability changes with flow. Flow-habitat curves are then used to define objectives for control of rainwater tanks and stormwater storages. This approach provides a pathway for adaptive, multi-objective stormwater systems that support stream health and biodiversity alongside water supply and flood protection.