Marine and estuarine habitat degradation threatens ecosystem function and delivery of ecosystem services. An increasing number of management interventions aiming to improve ecological condition within impacted marine and estuarine habitats are being implemented. Monitoring the ecological outcomes of management interventions to evaluate their effectiveness supports adaptive management. However, the lack of a standardised set of indicators has impeded reliable assessment and knowledge sharing. The objective of this research project is to develop a cross-ecosystem standardised indicator framework to assess changes in benthic habitat conditions. The rapid Marine and Estuarine Condition Assessment Tool (MarECAT) was developed for Queensland, Australia; however, it can be applied elsewhere. A literature review was undertaken to identify indicators and metrics for habitat condition assessment that were reviewed by subject matter experts through a series of Technical Group meetings. Three indicator groups were identified based on the presence or absence of structural macrobiota attributes (i.e., macroflora, macrofauna, and substrate-dominated). The panel of experts endorsed a list of 42 condition indicators with associated metrics representing all ecosystem components, enabling a comprehensive assessment of habitat condition for a rapid assessment tool. A level of confidence nominated by practitioners was allocated to each condition indicator metric to inform the interpretation of assessments. Another outcome of the expert workshops was the endorsement of 10 threat indicators representing key pressures in marine and estuarine habitats, along with a specific assessment scale. The scoring method developed for the MarECAT will facilitate reliable assessment of management intervention outcomes and implementation of adaptive management to improve project success.