The Nansha Islands comprise the largest atoll archipelago in the South China Sea that accommodates 15% of global atolls. In contrast to the reef flats of the Indo-Pacific region that commonly have grown close to modern sea level, a considerable portion of the atoll rims here consists of reef flats as deep as 6-20 m. To better understand whether these deep reefs are relict features abandoned by sea-level rise or host to modern physical reworking, we conducted an 8.5-month mooring observation of hydrodynamics on the 12-m-deep southwest-facing reef flat of Tiexian reef. These measurements show a predominance of seasonal-varying strong waves and stable currents, in line with short-term observations at three other deep-reef-flats nearby. While the reef flat was protected from the northeast monsoon from January to May, the southwest monsoon from June to September resulted in prolonged exposure to large waves and more vigorous cross-flat currents (mean Hs of 1.3 m; orbital velocity 0.22 m/s), resulting in consistently large near-bed shear stresses (mean of 0.6 N/m² on reef sediments and maximum of 18.9 N/m² on coral reefs) that are capable of entraining sediment for almost the entire monsoon season. Assuming a mere ratio of 1-10% mobile sediment would result in rim height deflation on the order of 0.5-5 cm/y. Such values similar to potential rates of reef accretion imply that modern processes could play a significant role in the maintenance of the deep reef flats, which can be surprisingly active environments with living coral colonies and coral debris coverage.