In this paper we present an application of a variational method for the reconstruction of the velocity field in a coastal flow in the central Adriatic Sea, using in situ data from surface drifters and outputs from the ROMS circulation model. The variational approach, previously developed and tested for mesoscale open ocean flows, has been improved and adapted to account for inhomogeneities on boundary current dynamics over complex bathymetry and coastline and for weak Lagrangian persistence in coastal flows. The velocity reconstruction is performed using nine drifter trajectories over 45 d, and a hierarchy of indirect tests is introduced to evaluate the results as the real ocean state is not known. For internal consistency and impact of the analysis, three diagnostics characterizing the particle prediction and transport, in terms of residence times in various zones and export rates from the boundary current toward the interior, show that the reconstruction is quite effective. A qualitative comparison with sea color data from the MODIS satellite images shows that the reconstruction significantly improves the description of the boundary current with respect to the ROMS model first guess, capturing its main features and its exchanges with the interior when sampled by the drifters. Copyright 2008 by the American Geophysical Union.