We derive some structural and spectral properties of regular bipartite graphs with three distinct non-negative eigenvalues. Next, we consider the relations between these graphs and two-class partially balanced incomplete block designs, and we present a number of situations when the graphs we consider are in fact the incidence graphs of those designs. As a consequence, we give a several constructions of connected regular bipartite graphs with six distinct eigenvalues, and we also determine all such graphs with degree 3, and all such graphs on at most 20 vertices.