A variational data assimilation system has been implemented for the tropical Pacific Ocean using an eddy-permitting regional implementation of the MITgcm. The adjoint assimilation system was developed by the Estimation of the Circulation and the Climate of the Ocean consortium, and has been extended to deal with open boundaries. This system is used to adjust the model to match observations in the tropical Pacific region using control parameters which include initial conditions, open boundaries and time-dependent surface fluxes. This paper focuses on problems related to strong adjoint sensitivities that may impede the model fit to the observations. A decomposition of the velocities at the open boundaries into barotropic and baroclinic modes is introduced to deal with very strong sensitivities of the model sea surface height to the barotropic component of the inflow. Increased viscosity and diffusivity terms are used in the adjoint model to reduce exponentially growing sensitivities in the backward run associated with nonlinearity of the forward model. Simplified experiments in which the model was constrained with Levitus temperature and salinity data, Reynolds sea surface temperature data and TOPEX/POSEIDON altimeter data were performed to demonstrate the controllability of this assimilation system and to study its sensitivity to the starting guesses for forcing and initial conditions.