The Nansha Islands comprise the largest atoll archipelago in the South China Sea, accommodating 15% of global atolls. In contrast to reef flats found elsewhere in the Indo-Pacific region that typically have grown close to modern sea level, a considerable portion of atoll rims there are composed of 10-20-m-deep reef flats. To better understand modern processes, particularly whether these deep reefs are host to modern physical reworking or instead may be relict features abandoned by sea-level rise, we conducted a mooring hydrodynamic observation from January to September on a 12-m-deep southwest-facing reef flat. These measurements show a predominance of seasonally-varying waves and stable, moderate tide-driven currents, similar to short-term observations at three adjacent deep-reef-flats. While the reef flat was protected from the northeast monsoon from January to May, the southwest monsoon from June to September caused prolonged exposure to large waves (mean Hs of 1.3 m; orbital velocity 0.22 m/s) and consistent cross-flat currents (0.08 m/s on average), resulting in near-bed skin-friction shear velocities of 0.02 m/s on average. These wave conditions are capable of forming and mobilizing bed ripples while entraining coarse coral sand (d50 = 1 mm) for over half a year. Estimates of potential sediment flux suggest the capability for combined waves and advective currents to deflate the 12-m-deep reef rim by up to 28 mm in 8 months. As these potential losses are similar to reef accretion rates, our measurements imply that modern processes could play a significant role in the maintenance of deep reef flats.