This article on 'How To Caulk a Toilet' will give some tips and instruction on sealing the base of your toilet to the floor. Whenever you remove your toilet, you will need to replace the caulking.
Toilets That Are Leaking at the Base
A word of caution about leaking toilets. Adding caulk around the bottom of a toilet is 'NOT' a solution for a leak. You will trap the water and cause other problems, not the least of which is rotting out your subfloor. If you have a toilet that is leaking around the base, see the article 'Fixing a Toilet Leaking at the Base'. You want to fix the leak as soon as possible to avoid further damage.
Reasons For Caulking the Toilet Base
There are two key reasons for caulking the toilet to the floor. First, you want your toilet to look like it belongs there. You will usually have an unsightly gap around the base if you do not caulk it.
The second reason it that you will invariably get some water on the floor. Mopping the floor, spills and dripping while we are drying off will get water on the floor. Water that gets under the toilet base cannot be cleaned up. It will produce unwanted odors. Caulking will keep the excess water out on the floor where it can be dealt with.
Choosing Caulk for a Toilet
You want to use a good quality 'Tub and Tile' or 'Bathroom' caulk for this job. This means it will be 'Silicone', probably 100%. Do not use standard painters or latex caulks for this job. Your bathroom is considered a 'wet' area, so you want caulk that will stand up to the moisture. A tube of this type of caulk will run between $5 & $10, it is best not to be cheap about this purchase.
Getting the right color is a concern. Ideally, the color of the caulk will closely match the color of the toilet. White is common of course, but many times people with have decorator colors for the bathroom fixtures. Talk to the staff at your paint supply store for assistance.
Preparation for Caulking
Silicone caulk is not the easiest stuff to work with. It 'Does Not' clean up with water. The best thing to use is a solvent, lacquer thinner is preferred by many. Silicone also requires some tooling (yes, that can be your finger).
First thing you want to do is prepare the area. Carefully clean the surfaces that the caulk needs to stick to. Use caution with solvents. You can ruin your flooring or other surfaces. Make sure the cleaning agent you use is compatible with the finishes around your toilet.
Once you have the area clean, you will want to tape off the surfaces that you don't want to get caulk on. If you are skilled at caulking, you can skip this step. However, most of us are amateurs and don't get enough practice to be skilled. Use blue or green tape on both sides of the caulk joint. When you tool the joint, the excess will harmlessly wipe off onto the tape.
Caulking Around the Toilet
Once you have taped off the joint so that you only get caulk where you want it, you are ready to start. You want to fill the gap completely, so make sure you get enough material into the joint. To do this, you will use a caulking gun. Keep a scrap piece of cardboard handy to set the gun on when you need to set it down. Release the pressure on the gun when you set it down. Even when you do that the caulk will continue to ooze out the end, so you want it dripping on something besides your floor.
Caulk all the way around the base of the toilet, making sure the joint is filled. Have a rag handy with a little solvent on it for when you start to tool the joint.
Don't wait to long before you smooth out the joint. Silicone will start to tack after a few minutes and the tooling will be more difficult. Use a joint tool or your finger to smooth and shape the joint to a pleasing look. Keep wiping off the excess caulk onto the rag.
When you have the joint completely tooled, you will want to give it a few minutes to set. After that, you can pull the tape off carefully. Pull the tape up and away from the joint in a continuous motion. Have a garbage bag handy to throw the tape away.
After the tape is removed, carefully clean away any caulk that got where you did not want it. You can also let the caulk dry and use a scraper or razor blade to remove it.
Try to let the caulk dry for 24 hours before you get it wet. Some caulks claim that they are waterproof in shorter amounts of time. Check the label to make sure.
See the article 'Fixing and Troubleshooting a Toilet' to make sure that the rest of your toilet components are functioning properly.