Drop shafts play a vital role in urban drainage and tunnel sewerage systems. To gain an insight into the magnitude of transient flow fluctuations inside a drop shaft attached to a scroll vortex intake, large eddy simulations (LESs) are performed in this study. First, the LES predictions are validated against experimental data from Guo (2012), demonstrating good agreement for both the time-averaged head-discharge relationship and the minimum air-core percentage. Subsequently, the transient fluctuations of the air core inside the drop shaft are investigated, with the worst-case scenario being choking of the air core inside the drop shaft, which might lead to a grave consequence to the system response. The transient fluctuations of the air core are found to have up to 13 % variation in the non-dimensional air-core area due to dynamic contraction and expansion. Additionally, velocity characteristics at different vertical and angular locations within the drop shaft are analysed, offering new insights into vortex structures and challenging assumptions from existing analytical models. The transient simulation results also reveal a global vortex structure together with embedded small-scale vortices using the $\Omega$-criterion vortex identification method.