The best way to deal with driving in rough water is to avoid it. Before going on the water, take an advanced course in navigation and weather, and practice your maneuvering skills. Learn everything you can about rough water conditions, how to read a barometer, how to shorten sail and other emergency drills. You can often avoid rough water conditions by listening to NOAA weather reports before heading out and by paying close attention to shoreside weather stations. Get to know what small craft warning and other high wind warning flags look like. For the safety of the people onboard and the vessel itself, become excellent at handling a boat in fair conditions and take no risks. If you're caught out on the water, a few basics are important to know.
Put on your PFD — personal flotation device — or life jacket as soon as rough weather is indicated. Have all necessary emergency equipment onboard before going out. Have nautical charts, especially if boating inland or near coastal waters. In other words, be prepared to meet any potential challenge or weather hazard. Each person needs to be wearing a PFD, ideally hooked on by jack lines.
Get the best helmsman behind the wheel or tiller. If you are alone, do not let go of the helm unless things worsen and you have an excellent autopilot that's been previously tested and verified. Watch the water, watch the wind and watch for traffic (other boats) and keep your horn handy in low visibility. Steering can become extremely challenging, and if you have little or no experience, the one thing to remember is not to panic.
Maintain just enough speed to maneuver and keep control of the boat. Flat-bottomed power boats respond completely differently than do deep keel sailboats. Know your boat. Every situation is different, so there is no one way to drive in rough weather because the conditions are constantly changing; you must remain alert constantly and respond cautiously. Don't make sudden speed increases or turn drastically or too fast. Stay calm.
Keep the bow or stern turned end onto the waves — this is tricky as it's hard to maintain, which means you have to hold on to the wheel and steadily respond to each wave or wind shift, whether under power or sail. Be extremely mindful of waves coming in from the beam (side) as you could broach or capsize. Sometimes it's OK to drive straight through smaller waves, but large following seas can push you into the wave ahead of you if the boat moves too fast. Reducing sail on sailboats will help, as in reefing, using a storm trysail or going bare poles (no sails at all) if the conditions force that.
Alter course and don't worry about getting to your destination unless you're on some chop on a small lake, and then carefully return to the nearest dock and tie up. If you were steering 215 at sea, and the weather forces you to turn the other way, do it. Just avoid coastlines, inlets, reefs and other boats no matter what. Keep your depth sounder on with the alarm set and use other navigation equipment as needed. Run with the wind, steering carefully and watching over your shoulder often.