We characterize fluctuations in atom number and spin populations in F=1 sodium spinor condensates. We find that the fluctuations enable a quantitative measure of energy dissipation in the condensate. The time evolution of the population fluctuations shows a maximum. We interpret this as evidence of a dissipation-driven separatrix crossing in phase space. For a given initial state, the critical time to the separatrix crossing is found to depend exponentially on the magnetic field and linearly on condensate density. This crossing is confirmed by tracking the energy of the spinor condensate as well as by Faraday rotation spectroscopy. We also introduce a phenomenological model that describes the observed dissipation with a single coefficient.