Also, check for a loose alternator belt!
Check for a loose alternator belt, and if you have a volt meter check the voltage output of your alternator. It should read somewhere between 13.8 and 14.5 VDC. 14.1 would be a benchmark reading. If you have trouble with battery recovery, it is better to charge at a higher voltage. Boats are notorious for having corroded connections. It is easy to determine the condition of your connections using a digital volt meter. Connect one lead to the alternator output and the other to your positive battery connection. It should read less than .2 VDC. If it reads more, there is too much resistance in the cable/connections. Check the ground cable from the engine to the battery using the same procedure. If you have battery selector switches or other components you can check the entire circuit as stated, and then check each leg to isolate the problem. If your problem still exist after checking/repairing the charging system, you can test your switches and loads using the same technique.You can purchase an inexpensive digital volt meter at Sears, Harbor Freight, Norther Tools, or any number of tool stores. Be careful not use an inexpensive meter on electronics, unless it says that it has 10 mega ohm impedance. If the meter passes current, it can "toast" electronics. Nevertheless, an inexpensive meter will work fine on starting, charging, and lighting systems.