In this paper a 3-D reconstruction method is proposed of sea bottom topography, i.e. bathymetry, for sonar data in highly reverberant and multi-path underwater environments. Recent publications showcase the negative impact of waves involving sea surface reflections on the sea bottom imaging process. The novelty of our proposal is twofold: firstly it relies on the use of Markovian-model based processors for bahymetric reconstruction and involves data association filters. Secondly, we propose a nearest neighbor version of the Integrated Probabilistic Data Association filter, capable of filtering several echo trajectories in the presence of clutter with a relatively reduced complexity compared to other existent methods.