The invention is a hydrogen generator with a liquid reservoir, a reaction area, a byproduct containment area and a hydrogen containment area within a housing. A liquid from the liquid reservoir can react within the reaction area to produce hydrogen gas and byproducts, which flow to the byproduct containment area, and hydrogen gas passes into the hydrogen containment area and is released from the housing through a hydrogen outlet as needed. The liquid reservoir and the reaction area are each within a container made of a liquid impermeable material, the byproduct containment area is within a flexible container made of a hydrogen permeable, liquid impermeable material, and the hydrogen containment area is within a flexible container made of a hydrogen impermeable material. The byproduct containment area is in a volume exchanging relationship with one or both of the liquid reservoir and the reaction area.