Charts need to stay attached to the boat, and they are best secured by putting them in a transparent case.
Several companies produce waterproof chart cases. They work pretty well if you are careful when closing the seal. However, it's a good idea to waterproof your charts even if you use cases, since water creeps in, even if only as condensation. If the chart case doesn't have clips, you will need some; don't depend on your deck bungies to hold the case securely on deck. Your local marine hardware dealer will have a selection of small stainless-steel carabiners or snap hooks. The smallest has a waist at one end so that it can go on a D-ring, then be lashed into place. I like the sailing carabiners so well that I have them on all deck and cockpit gear. Their extra cost is worth it. The smaller the chart case, the more times you need to fold the chart, so I usually go for the biggest chart case that will fit on deck without hanging over the side. The cases that are about 16" by 22" allow a NOAA chart to be folded into quarters if you trim the vertical margin off to just the latitude line.

The new plastic charts keep you from having to waterproof paper. They are a bit more expensive than NOAA charts, but they cover more area and have a second chart on the back. Compass roses will stick to these plastic charts and waterproof markers will work if you let the ink dry carefully. These charts are very durable; one that I use all the time finally died after two seasons of being unceremoniously stuffed under the bungies on my foredeck. While they sort-of stick themselves to the deck when they get wet, it's still best to put them in a chart case to keep them from getting damaged or lost. For special navigation situations, I often carry topographic maps for the area, in addition to the navigational chart. The advantage is that they have a scale of 1:25,000, which provides better shoreline detail. While they indicate depths, their disadvantage is that there is no navigational information printed on them. Of course, you can write them on the chart, but it is a lot of work.

Fortunately, photocopies can be waterproofed. In some areas, you may find the year's tide tables printed in small, waterproof booklets. They are ideal for carrying on deck if you have young eyes. For my old eyes, the type is too small to read, so I find it useful to keep a simple plastic magnifier in my chart case. It's nothing more than Fresnel lines inscribed on a piece of plastic. The one I use is designed for navigation and has a scale on one side. You can find one of these in a marine supply store. I keep a compact backpacker's compass in my PFD pocket. For taking bearings, it is easier to use a backpacker's compass than to maneuver the boat to use a deck-mounted compass. This hand-held compass is also handy for checking the deck-mounted compass, in case I've put the radio or a propane cylinder too close to it, making it inaccurate. It is also there as a backup and for use on land, whether you take a hike or want to take bearings from the beach. Besides charts, you need tools to measure bearing and distance. People talk about kayak navigation as an art, not a science so, to be artful, try using your hands as tools. Try various finger joints, finger extensions, finger widths and hand spans against the scale of your charts. You will likely find something that is close to a mile, and something that's close to five miles. For example, on a 1:40,000 chart, my hand span is about five miles; the distance from the tip of my thumb to the first knuckle is a mile; and the distance between my index finger and little finger when held out straight is two miles. With practice, you can use the side of your forefinger or the back of your hand to transfer bearings between the compass rose and a particular spot on the chart. Keep your wrist locked straight and use your shoulder muscles to move your hand. Move your hand from the compass rose to the bearing that you want, or from the bearing line to the compass rose. You will be surprised how easy it is to hold the angle you need, within five degrees or so.
It might not be up to Coast Guard or Power Squadron standards, but you'll always have the tools.

Most of the standard devices for figuring distance/direction on a chart are too complex for use on the deck of a kayak. The exception is the Small Craft Nav-Aid developed by Chuck Sutherland specifically for kayaking. It is a 4" x 5" piece of clear plastic with a compass rose and reciprocal rose on it. A piece of monofilament is fastened to a hole in the center. The user marks the plastic, using a waterproof marker, with lines that show true north-south and east-west directions, according to the variation of their local region. When these lines are lined up with latitude or longitude lines, the rose points to magnetic north, and the monofilament can be stretched out along a course, or bearing line. Bearings and back bearings can be read directly. The monofilament can be marked according to the chart's scale, so that distance can be read directly along the mono-filament. If you attach a light string lanyard that you mark with miles, the string is easy to place along a convoluted route to estimate paddling distance. I usually carry a spare Nav-Aid, since mine, over time, have faded, been broken or had the monofilaments pulled out. If the monofilament pulls out, the center hole can be enlarged slightly and another light string substituted. You can make a device similar to the Nav-Aid from a one-armed protractor commonly found in a marine supply store.
The small C-Thru (# 255A) is especially handy for this do-it-yourself project. These come in two sizes: 7" in diameter and 3.5". First, cut the movable protractor arm off. (Save the cut-off arms, as these are usually marked with scales, and are useful additions to your chart bag.) I leave a small tab on the remaining part of the protractor so I can punch a hole in it for a lanyard. Thread a thin, colorful piece of braided cord through the hole in the center of the protractor and knot the end. I like to knot it on both sides of the hole. Mark the protractor with true north for the chart you'll be using.