The primary scientific goal of neutrino telescopes is the detection and study of cosmic neutrino signals. However, the range of physics topics that these instruments can tackle is exceedingly wide and diverse. Neutrinos coming from outside the Earth, in association with other messengers, can contribute to clarify the question of the mechanisms that power the astrophysical accelerators which are known to exist from the observation of high-energy cosmic and gamma rays. Cosmic neutrinos can also be used to bring relevant information about the nature of dark matter, to study the intrinsic properties of neutrinos and to look for physics beyond the Standard Model. Likewise, atmospheric neutrinos can be used to study an ample variety of particle physics issues, such as neutrino oscillation phenomena, the determination of the neutrino mass ordering, non-standard neutrino interactions, neutrino decays and a diversity of other physics topics. In this article, we review a selected number of these topics, chosen on the basis of their scientific relevance and the involvement in their study of the Spanish physics community working in the KM3NeT and ANTARES neutrino telescopes.