The Borneo vortex (BV) is a synoptic‐scale vorticity feature found in the South China Sea near Borneo during extended Boreal winter, which can bring heavy rain to the region. Predicting this rainfall is difficult. Therefore, a better understanding of the structure of these vortices and their interaction with equatorial waves could aid forecasters. Here we divide the BVs found from 41‐years of October–March ERA5 data into five clusters based on their tracks identified using relative vorticity maxima. These clusters capture distinct phenomena: vortices moving westwards across the South China Sea, vortices tracking along the north and northwest sides of Borneo, vortices sitting on the west side of Borneo, and vortices that initiate on the northwest side of Borneo, cross the equator and track eastwards along the south coast of Borneo. These clusters have a strong seasonal dependence related to the strength and southward propagation of the northeasterly flow and therefore cold‐surge type. The Madden–Julian oscillation (MJO) is considerably less important than the cold surge for modulating vortex frequency but has a similar order of magnitude impact on vortex rainfall. Kelvin waves strongly modulate rainfall from all BVs. Westward‐moving mixed Rossby–gravity (WMRG) and Rossby n = 1 (R1) waves modify frequency, rainfall, and vorticity through modification of environmental vorticity and northeasterly flow. These properties are highest when the BV is within or on the leading edge of the positive vorticity phase of R1 waves (in the northern hemisphere) or WMRG waves. Westward‐moving vortices north of 4° N are often embedded in and move with R1 or WMRG waves. Examining case studies in detail, we find BVs typically extend upward to 500–400 hPa but can reach to 300 hPa, and those near the equator may not always have closed streamlines. Under vertical wind shear they may tilt, usually to the west.