We study the Picard-Lefschetz formula for the Siegel modular threefold of paramodular level and prove the weight-monodromy conjecture for its middle degree inner cohomology with arbitrary automorphic coefficients. We give some applications to the Langlands programme: Using Rapoport-Zink uniformisation of the supersingular locus of the special fiber, we construct a geometric Jacquet-Langlands correspondence between $operatorname{GSp}_4$ and a definite inner form, proving a conjecture of Ibukiyama. We also prove an integral version of the weight-monodromy conjecture and use it to deduce a level lowering result for cohomological cuspidal automorphic representations of $operatorname{GSp}_4$.