Obi-Wan's lightsaber shorts out when he gets it wet in the swamp after escaping his landing craft. Lightsabers require special modifications, or else they don't work underwater, this is an established EU fact.
This is the reason he is running from the STAPs and why Qui-Gon has to rescue him. I feel like I've seen a deleted scene with this in it, but it may just be that the scene has been described in other sources.