A variational study of two-nucleon systems with lattice quantum chromodynamics is performed using a wide range of interpolating operators: dibaryon operators built from products of momentum-projected nucleons, hexaquark operators built from six spatially localized quarks, and quasi-local operators inspired by two-nucleon bound-state wavefunctions in nuclear effective field theories. Correlation-function matrices involving products of these operators are constructed by computing timeslice-to-all quark propagators with sparsening techniques. Comparisons between results obtained using the same gauge-field ensemble but different interpolating-operator sets demonstrate that interpolating-operator dependence can lead to significant effects on the two-nucleon energy spectra obtained using both variational and non-variational methods.