The effects of a priori parameters on the error subspace estimation and mapping methodology introduced by P. F. J. Lermusiaux et al. is investigated. The approach is three-dimensional, multivariate, and multiscale. The sensitivities of the subspace and a posteriori fields to the size of the subspace, scales considered, and nonlinearities in the dynamical adjustments are studied. Applications focus on the mesoscale to subbasin-scale physics in the northwestern Levantine Sea during 10 February-15 March and 19 March-16 April 1995. Forecasts generated from various analyzed fields are compared to in situ and satellite data. The sensitivities to size show that the truncation to a subspace is efficient. The use of criteria to determine adequate sizes is emphasized and a backof- the-envelope rule is outlined. The sensitivities to scales confirm that, for a given region, smaller scales usually require larger subspaces because of spectral redness. However, synoptic conditions are also shown to strongly influence the ordering of scales. The sensitivities to the dynamical adjustment reveal that nonlinearities can modify the variability decomposition, especially the dominant eigenvectors, and that changes are largest for the features and regions with high shears. Based on the estimated variability variance fields, eigenvalue spectra, multivariate eigenvectors and (cross)-covariance functions, dominant dynamical balances and the spatial distribution of hydrographic and velocity characteristic scales are obtained for primary regional features. In particular, the Ierapetra Eddy is found to be close to gradient-wind balance and coastal-trapped waves are anticipated to occur along the northern escarpment of the basin.