In response to an external stimulus, the cochlea emits sounds, called stimulus frequency otoacoustic emissions (SFOAEs), at the stimulus frequency. In this article, a three-dimensional computational model of the gerbil cochlea is used to simulate SFOAEs and clarify their generation mechanisms and characteristics. This model includes electromechanical feedback from outer hair cells (OHCs) and cochlear roughness due to spatially random inhomogeneities in the OHC properties. As in the experiments, SFOAE simulations are characterized by a quasiperiodic fine structure and a fast varying phase. Increasing the sound pressure level broadens the peaks and decreases the phase-gradient delay of SFOAEs. A state-space formulation of the model provides a theoretical framework to analyze the link between the fine structure and global modes of the cochlea, which arise as a result of standing wave resonances. The SFOAE fine structure peaks correspond to weakly damped resonant modes because they are observed at the frequencies of nearly unstable modes of the model. Variations of the model parameters that affect the reflection mechanism show that the magnitude and sharpness of the tuning of these peaks are correlated with the modal damping ratio of the nearly unstable modes. The analysis of the model predictions demonstrates that SFOAEs originate from the peak of the traveling wave. [ABSTRACT FROM AUTHOR]