A limited-area ocean prediction system is developed to acquire forecast error covariances related to uncertainty in atmospheric forcing and turbulent mixing using perturbed model parameters within an Ensemble Kalman Filter (EnKF). The system performs sequential data assimilation delivering realistic ocean state estimation and forecasts. It is initialised to observations using the EnKF, the hybrid-EnKF and Ensemble Optimal Interpolation (EnOI). It has higher resolution than the parent global model, includes tides and assimilates altimetric sea level anomaly to constrain the offshore mesoscale circulation. Dynamic ensemble spread introduced by parameter uncertainty shows agreement with error estimates obtained from forecast innovation statistics. Hybrid EnKF offers improvements to both EnKF and EnOI, having smaller analysis increments and forecast errors. The ensemble mean of the hybrid-EnKF is more accurate than any member due to the introduction of parameterised error which behaves as additive inflation in the hybrid EnKF system. This indicates the parameterisation acts as a non-linear filter for model forecast error growth. To demonstrate consistency, experiments are carried out for various regions that differ in their oceanographic situations. The hybrid EnKF data assimilation system enables practical use of dynamic ensembles that capture the flow dependent errors which are mixed with static or climatological covariances for situations where model error is systematically under-estimated.