Cut out and replace water-damaged subfloor sections before you do any further bathroom remodel work.
Start by confirming the extent of damage with a firm probe using a screwdriver or awl to find soft areas and check under fixtures and around drains for moisture pockets. Remove finish flooring and any underlayment until you reach solid wood, then mark and cut out only the compromised plywood to maintain maximum structure. Measure and cut replacement plywood that matches the existing thickness exactly so the finished floor stays level, and fasten new panels to joists with construction screws every six inches along edges and every eight to twelve inches in the field for a secure, rigid surface. Before installing new decking, dry and vacuum the joist bays and apply a mold treatment to affected framing and surrounding sheathing following product instructions and allowing full drying time to avoid trapping moisture. Install blocking between joists where edges of replacement plywood meet to prevent flex and to provide secure screw placement, and use construction adhesive on seams for added stiffness and to reduce squeaks. Finally, check for level across the repaired area with a straightedge and sand or plane any high spots then add a waterproof membrane or appropriate underlayment before you reinstall finish flooring and fixtures.
One common mistake is cutting out too little and leaving marginally damaged wood that leads to recurring rot; solve this by probing broadly and removing any area that feels spongy or has visible discoloration until you reach clean, tight wood. Another issue is using replacement plywood of the wrong thickness which causes uneven flooring and stress at seams; always measure existing panels and purchase or mill exact thickness and use tapered shims only when absolutely necessary then plane for a flush fit. A third problem is inadequate mold treatment or sealing which allows spores to persist under the new subfloor; address this by cleaning with a fungicidal product approved for structural wood, allowing full drying, and using a mold-resistant primer or sealant on exposed framing before covering.
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