This is a transient model, the negative balance number means there is water removed from the model volume, and amount of inflow is not enough to maintain the original volume of water in the model. The water levels in your model should be declining. Eventually, the water levels should stabilize; it is possible that the model will dry out. If the water levels are not declining (unchanging or oscillating up/down or rising) then your model is probably unstable and has a major problem that needs fixing before it will work properly. An important factor is the initial water levels you specified.
Pete