Direct numerical simulations (DNSs) of open-channel flows in the presence of an air–water interface were performed to examine the effects of interface deformation on the turbulence structures. In the water-driven turbulence, flows characterized by either of the two Froude numbers (Fr = 0.2 and 0.8) were examined and compared. A coupled level-set and volume-of-fluid (CLSVOF) method was employed to track the interface. The mean and root-mean-square of the air–water interface elevation varied rapidly with the spanwise distance as Fr increased. The air that contacted the water was entrained into the turbulent flow. At high Fr, all turbulent normal stresses on the air side of the interface were high near the sidewall. Two-point correlations between the streamwise vortex and the velocity fluctuations provided structural information about the near-wall streaky structures and the inner secondary flows in the cross-stream plane. Linear stochastic estimates of the conditionally averaged flow field showed that the inner secondary flow consisted of not only in-plane velocity components but also streamwise velocity components.