Using an improved numerical code we investigate the creation and evolution of quantum knots and links as defects of the Gross–Pitaevskii equation. The particular constraints put on quantum hydrodynamics make this an ideal context for application of geometric and topological methods to investigate dynamical properties. Evolutionary processes are classified into three generic scenarios representing (i) direct topological cascade and collapse, (ii) structural and topological cycles, and (iii) inverse topological cascade of complex structures. Several examples and test cases are studied; the head-on collision of quantum vortex rings and the creation of a trefoil knot from initially unlinked, unknotted loops are realized for the first time. Each type of scenario is studied by carrying out a detailed evaluation of fundamental geometric and dynamical properties associated with evolution. Direct topological cascade that governs the decay of complex structures to small-scale vortex rings is identified by writhe measures, while picks of total curvature are found to provide a clear signature of reconnection events. We demonstrate that isophase minimal surfaces spanning knots and links have a privileged role in the decay process by detecting surface energy relaxation of complex structures. Minimal surfaces are shown to be critical markers for energy and prove to be appropriate detectors for the evolution of complex systems.