The Murray-Darling Basin in south-eastern Australia is subject to the compounding effects of river regulation and drought. The recent decade-long Millennium Drought saw large-scale changes in environmental conditions, degrading ecological communities and reducing species occurrence. With limited recovery of many communities post-drought, predictive habitat models were developed and field-validated to investigate the relationship between two key submergent macrophytes (Myriophyllum salsugineum and Vallisneria australis) and the environmental variables influencing their occurrence, using the Lower Lakes in South Australia as a case study. Telemetered records of logged environmental variables were paired with vegetation monitoring data to develop non-parametric multiplicative regression models. The influence of the intra-seasonal variation in conductivity and water temperature from the telemetered records, in conjunction with water pH from field surveys, were found to define the habitat envelope for those species. Therefore, these variables are potentially limiting species occurrence post-drought. These findings provide managers with regional predictions of species responses that can be incorporated into management decisions to ensure submergent macrophyte assemblages remain viable into the future, while providing a proof-of-concept for a modelling approach that can be undertaken to describe similar relationships for other key taxa within the Murray-Darling Basin and elsewhere.