If installed correctly, glass blocks offer a more waterproof way to provide light in any areas of your house that are exposed to a high amount of moisture or precipitation. The glass blocks allow light to pass through but provide a thick barrier against the water. Still, the mortar between the blocks can be a source of weakness, allowing water to leak into your house even if the glass blocks themselves are not damaged.
The kind of mortar you use between your glass blocks affects how resistant to moisture the window or wall will be. Regular mortar, or the kind you would use for bricks, does not seal out moisture to the same degree as mortar made of Portland cement and sand, according to home improvement expert Tim Carter.
When applying the mortar to the blocks, the key is to ensure maximum coverage and to protect against gaps or air pockets in the mortar. Pack mortar into the seams between the glass blocks using any "tool" that will do the job, from sticks to your own hands (protected by rubber gloves). Getting mortar on the surface of the blocks is not a problem because you can wipe it off with a wet sponge before it completely dries. When you're finished stacking the blocks, don't apply mortar to the top. Instead, close the gap above the blocks with silicone caulk. Mortar may put too much pressure on the blocks, leading to cracks and leaks down the road.
After the glass block’s mortar has fully cured, which can take up to five hours, silicone caulk applied to the seams will provide another seal against water intrusion, in case the mortar has cracks or gaps. The caulk should be applied to the seams between the blocks and between the blocks and any materials the blocks touch. It needs to cure for at least 24 hours in dry and warm weather, and even longer in cool or wet weather, before you touch the glass blocks or the caulk. Contacting the caulk before it cures completely may disrupt its seal with the glass, destroying its waterproof qualities.