Make sure your feed pump is properly installed, check regularly for vacuum leaks, do not allow air to enter your thru hull, and fresh water flush your system after every use.
The feed pump is the workhorse behind your watermaker, and taking care of it will ensure a long lasting watermaker with few replacements and lots of good quality fresh water in your tanks. Most pump problems come from improper installations. Make sure the feed pump is mounted as low as possible in your boat and as near to the thru hull is your space will allow. If your system uses booster pumps, they must be installed below the waterline, and as near to the thru hull as possible. Check the intake hoses regularly for vacuum leaks, or signs that the pump is sucking air. Do not operate your system in heavy weather if there is a chance that the thru hull will lift clear out of the water, or if there is significant aeration of the ocean due to wave activity. Flushing your watermaker with fresh water after each use will dramatically reduce corrosion problems with stainless steel pump heads, and also keep the membrane free from biofouling, which will also help extend the pump life.