Previous studies have shown only modest effects of supramammillary nucleus (SuM) dysfunction on theta frequency and learning in the water maze (WM), with larger effects in other tasks. However, theta recorded from SuM, and used to trigger the production of theta-like oscillations in the hippocampus, produced reversal of the deficit in WM learning produced by theta blocking. We explored this apparent inconsistency by analyzing the relationship between SuM and hippocampal theta in the control group of this theta-blocking experiment using coherence, phase analysis, and the directed transfer function. We found little evidence of an influence of SuM on the hippocampus in the bulk of WM learning-with some possibility of SuM becoming involved briefly later in learning. A learning-related increase in coherence was observed in conjunction with gradual phase reorganization of hippocampal theta in relation to SuM theta. This change in phase dynamics between the two structures was also correlated with a relative increase of the estimated direction of theta propagation from the SuM to the hippocampus. These results are consistent with the previous weak effects of SuM lesions and suggest that the use of SuM as a source to trigger hippocampal theta and recover function is likely to be due to coherence between SuM and some other structure that normally controls hippocampal theta during WM learning.