The main objective of this paper is to investigate the overall balance of momentum and energy within the Indonesian Seas to better understand the factors that control the total transport of the Indonesian Throughflow. Two models are used in the investigation: a "first-step" heuristic channel model and a more sophisticated "second-step," barotropic numerical model that incorporates high-resolution coastline and bottom topography. The experiments show that the barotropic model develops typical horizontal circulation patterns for the region. An analysis of the overall momentum and energy balances suggests that the total transport of the Indonesian Throughflow does not depend exclusively on the inter-ocean pressure difference but on other factors, including local winds, bottom form stresses, and the resultant of pressure forces acting on the internal sides.