The Rupelian Boom Clay in Belgium is a marine sedimentary deposit with an extensive data set. Astronomical control on high-frequency cyclicity has been proven before, and sedimentological analyses have shown climate-driven cycles caused by sea-level fluctuations. A long cycle in grain-size and bed thickness, involving the entire Boom Clay section, is related to tectonism. Shorter-duration low-frequency cycles, attributed in the past also to climate-driven eustasy, show a relationship with sediment supply expressed by bed thickness but related to tectonism. This apparent contradiction is studied by measuring the thickness differences of the individual Milankovitch-related (astronomical) beds in several wells with the thickness of the same bed in a reference well in the area. Such an approach eliminates eustasy as a controlling factor in the observed cyclicity patterns. Cumulative differential evolution maps of the basin are provided, and the evolution of the relative subsidence in all individual wells through time is visualised as cumulative-difference curves. Both approaches demonstrate that the levels considered in previous studies as controlled by eustasy in fact reflect tectonic history.