Sealing decking gaps. HELP

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I have recently built raised decking using scaffolding boards, pine I think, as decking. I wish to use the space underneath for storage but need to seal the gaps first. Can't use a membrane due to the support beams being below the board level. Have used silicone but can't paint over it effectively and wood filler just cracks. The gaps vary from 2mm to around 5mm. Any advice greatly appreciated.
 
Short answer is you can't / shouldn't and whatever you do will just leak and cause water to pond on the decking and cause it to rot and algae growth.

If you really do want it waterproof you need to lift all the decking, install a new base similar to a flat roof (Eg two layers of ply overlapped with a membrane on top or similar), then put the deck boards back down. You'd still have issues with the boards sitting in water and rotting though.
 
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