Final answer:
The primary source of the increased weight of the plant is water.
Step-by-step explanation:
The primary source of the increased weight (mass) of the plant in Jean Baptiste van Helmont's experiment is water. When he watered the plant regularly over the course of five years, the plant absorbed water through its roots, which contributed to its growth and increase in weight. The small decrease in weight of the soil is not significant compared to the substantial increase in weight of the plant.