Choose fresh flowers that are open, but not wilted, torn or brown around the edges. Any small imperfections will be magnified once the flowers are submerged. Roses, orchids, calla lillies, tulips and gerbera daisies all work well in submerged arrangements. Look for flowers without pollen and that don't have especially thin petals.
Remove any dead or damaged leaves or petals. Pinch any leaves or petals that need to be removed and gently pull them off the flower.
Choose a glass container that is slightly larger than the height and width of your planned arrangement. Keep in mind that you will want at least an inch between the top of the container and the bloom. Blooms can touch the sides of the container, and the exact size of the container depends on the look you want. For example, choose tall cylindrical containers for long-stemmed orchids and calla lillies, and short round containers for a tightly packed gerbera daisy bouquet. Clear glass containers are usually used for submerged flowers. Tinted glass can create a different look, but will obscure many of the details gained by submerging flowers.
Cut stems to the length of the container using sharp scissors. Make the cut at a 45 degree angle to allow the flower to better absorb water. Cut the stem short enough that the blooms will be below the top of the container when they are placed inside.
Place the flowers in the glass container, noting which parts of the stem and leaves come in contact with the bottom of the container.
Remove the flowers from the container, being careful not to break or damage any of the blooms.
Dab a small bead of glue on the stem and leaves at the point where they made contact with the bottom of the container. Hot glue is quick and easy, and usually can be pulled off and re-applied if you decide you aren't happy with the arrangement, but may only last a day or two once the water is added. Aquarium glue takes longer to set and won't allow you to correct mistakes once it is set, but the bond will last longer than the flowers will, which is ideal if you are creating an arrangement you expect to last more than a few days.
Place the flowers back in the container, carefully pressing the stem and leaves against the bottom to help the glue adhere. Don't wait too long between applying the glue and placing the flowers.
Add decorative stones to the bottom of the container, taking care to drop them in gently so they do not damage the flowers. Match the size, shape and color of the decorative stones to the container and flowers. Dime-size decorative glass stones sold in floral and craft supply stores are ideal.
Fill the container with distilled water, pouring slowly down the side of the container so that the water is not poured directly on to the blooms. Distilled water will not form bubbles that cover the blooms.
Arrange any flowers, leaves or stems as desired by gently pushing them into place with the handle of a wooden spoon or clean stick. Avoid using your hands, which will introduce natural oils into the water. A wooden spoon or stick is also less likely to damage delicate petals than hands or metal tools.