Yes your batteries are more than likely the root cause for this problem. How old are the batteries? Also make sure that when the boat is in storage that the battery switch is turned to the off position. Also make sure that the amp is wired to the battery switch. Amplifiers & stereos have a constant draw for the preset memories( radio stations & such). If the amp or stereo is not wired through the battery switch they can draw down the battery over time leaving you with a battery that is not fully charged. If the batteries are over 4-5 years old it is recommended to replace with new. For carbuerated motors use a deep cycle battery. For fuel injected motors you will need to run a cranking battery. I have always had great success with Interstate batteries for my customers.
I have a sony stereo powered by a 1000 watt amp with 8 polk audio speakers and a subwoofer in my boat. The sub has a capaciter. When i first get out on the water and try turning up the volume it cuts out. After 30 minutes or so, it seems to work fine. I know the system draws a lot of power and my theory is that my battery eventually gets fully or better charged from the alternator to where the stero works properly. Could this be solely a battery issue? The boat has two batteries and before and I have tried running it on 1, 2 or all at first but still no luck when I first get started. I wanted to make sure it was the batteries no being charged before I go drop $250 - $300 for new marine grade batteries. Thanks.