This study focuses on characterizing a discontinuity within the Seán stalagmite (4.75–7.75 cm) by means of two nondestructive techniques: (1) high-resolution micro-computed tomography (micro-CT) and (2) X-ray fluorescence (XRF) core scanning (XRFCS). Micro-CT was used to study the stalagmite density, and XRFCS was applied to obtain the qualitative elemental composition and colour measurements. The new data obtained from nondestructive techniques have been combined with previously published geochemical data and fabric determinations from the same stalagmite found in Sa Balma des Quartó cave in Mallorca. The two methodologies applied in the present study have improved the characterization of the distinctive horizon. The micro-CT images identified the layer as a minor event due the high air content. The distinctive horizon is characterized by a high Ti-content, indicating the arrival of terrigenous particles. Based on those observations, together with the fact that the micrite layer appears filling the gaps between the older columnar fabric, we argue that the micrite layer may represent a major flooding event inside the cave after the year 1616 ± 23 CE and before the year 1623 ± 28 CE, which can be related to an extreme rainfall event. This hypothesis is further supported by the observed cave flooding during the autumn of 2018.