If a proposed development is in a flood zone or overlay, such as the Special Building Overlay, a planning permit is required for subdivision or buildings and works.
This means, that as a part of the planning permit assessment process, the council will refer the planning application to the relevant floodplain management authority (your CMA or Melbourne Water) for review. They have 28 days to respond to the council about the proposed plans, and either object, approve or approve with conditions.
To locate your relevant FMA/CMA and get contact details, use this Interactive Map of Floodplain Management Authorities (FMAs/CMAs) in Victoria.
Source: Floodplain Planning by the State of Victoria