A study of the simulation of the Orinoco Low-Level Jet (OLLJ) and the cross-equatorial moisture transport over tropical South America using the Weather Research and Forecasting (WRF) model is presented. The focus is on the diurnal cycle and monthly means during one December-January-February (DJF) season (2003–2004). The sensitivity of the OLLJ and cross-equatorial moisture transport to the representation of surface fluxes and turbulence is explored by using two different Land Surface Models (LSM) and three Planetary Boundary Layer (PBL) schemes. Different LSMs produce large differences in the sensible heat flux over the Orinoco basin, but no substantial differences in the flow at the entrance of the OLLJ. However, these changes in surface fluxes were associated with a change in the low-level pressure gradient between the Orinoco and Amazon basins, and with up to 10% change in the simulated cross-equatorial moisture transport. The largest effects from different PBL schemes were found in the low-level flow near the Andes cordillera, and on the low-level southward cross-equatorial flow during the daytime. One of the PBL schemes exhibited a reduced moisture transport on the eastern flank of the Andes but enhanced southward transport around the core of the cross-equatorial moisture flux. Another PBL scheme produced a stronger net cross-equatorial moisture transport, with enhanced precipitation over the Andes-Amazon region by up to 30% during the afternoon and up to 13% in the daily mean. Improved observations over the region are needed to evaluate which combination best represents the flow.