ask to Wade Crow and/or Fan Chen, they made a study with SWAT and the EnKF:
Chen, F., W.T. Crow, P.J. Starks and D.N. Moriasi, "Improving hydrologic predictions of a catchment model via assimilation of surface soil moisture," Advances in Water Resources, 34(4), 526-536, 2011.
send them an email, they will surely answer you with all the details.