The subinertial flow of the Cozumel Channel is examined with nearly six months of current, subsurface pressure and meteorological data in order to (a) verify the validity of the geostrophic balance in Cozumel Channel and analyze the influence of other terms of the momentum equation in observed ageostrophic variations, and (b) estimate the transport through the Channel using a set of continuous current profile observations at the Channel's center and the cross section velocity maps obtained from shipboard ADCP observations. Over periods longer than a month, the momentum balance in the channel is mainly geostrophic, but on alternative periods of similar duration, intense ageostrophic fluctuations are found that have timescales of days to weeks and up to 1 m/s amplitudes. There is evidence that the advective nonlinear terms are the most probable cause of the lack of geostrophy over these periods. Other terms such as the local acceleration and the wind stress are found to contribute minimally in the ageostrophic fluctuations. A mean transport of approximately 5 Sv toward the Gulf of Mexico is estimated for the 5 months of measurements (December 1996 to May 1997), although with great variability: a minimum of 1.3 Sv around January, a maximum of 7.5 Sv by the beginning of May, and a standard deviation of 1.2 Sv. Neither surface currents nor the geostrophically deduced current is suitable for estimating the observed transport in the Channel.