Water intrusion into your boat can almost always be traced to a few relatively simple causes.
Recently, a former client contacted me with concerns about his powerboat taking on water. After replying to him with some information and suggestions I realized my comments could apply to most situations where leaks are a concern in a fibreglass boat. So here is my reply to him with a few edits and additions for context:
Your boat has a number of through-hulls built into the structure (or added later) that are necessary for the operation of some of your boat's systems. Not surprisingly, these through-hulls can be a source of leaks, so checking each one is a good place to start. If you are not already, I would close all sea-cocks when the boat is left unattended (a good practice regardless). If the leak stops with the valves closed you will have narrowed it down to the hoses and connections associated with the through-hulls that you closed. Now check each one from end to end - loose or broken hose clamps are the likely culprit.
If the leak didn't stop with the seacocks closed, check the through-hull fittings for a watertight seal against the hull and at the threaded connection with the seacock.
Next, check all the other hull penetrations and their connected gear - shafts, rudder posts, drain plugs. The propeller shaft penetrations are a very common source of water ingress. If the stern gland is the dripless type it should not let water in if functioning properly. If it is an older style with a packing gland, a slow drip (once every 30 seconds or so) should be all the water coming in. If you can't get a definitive look, when the vessel is next hauled out (with water in the bilge above the seals) more than a small amount of water dripping from the shafts is a sign that your problem may be here.
The wet exhaust is also a common source of leaks. When the engines are running your boat is continually drawing in seawater and pumping it out again through your exhaust system (keel cooled boats excepted). A leak anywhere in this system will result in water ingress into the boat - sometimes at an alarming rate. If the boat is taking on water when unused at the dock or on a mooring this is not likely your problem, but if the water is rising only when the engine is running, this is a good place to start looking.
Finally, your source of "leaks" may not be from outside the boat at all. The freshwater, grey water (sinks and showers), and blackwater (sewage) systems are a very common source of water in the bilge. Check these systems from end to end with particular attention to the hoses and connections. If there is a bad smell, suspect the grey water system. If there is a really bad smell, the source is likely the black water system.
If there is unexplained water in your bilges the chances are good that the source is one of the above. Be methodical and thorough in your inspection and you will likely discover the problem fairly quickly.