Can I charge the battery (1.2Vx2) with the suction tube submerged in the water or do I have to remove the suction tube every time I have to charge the battery?
Since you don't mention the model of the pump, if you can connect the charger with a dry connection, you should not have to remove the pump/tube. If you have to take the battery out, you stand the risk of dropping it in the water putting it back, but obviously (I think) you don't have to remove the pump/tube.
