Circadian clocks allow organisms to optimize their phenotypes in relation to rhythmic environmental conditions. Clocks must synchronize, or entrain, to environmental signals called zeitgebers (such as light and temperature) while maintaining internal rhythms that are robust to environmental noise. We know surprisingly little about how clocks function in the presence of multiple zeitgebers, although these are the conditions that exist in nature. Misalignment between zeitgeber cycles (here, "sensory conflict") can disrupt circadian rhythms in behavior and gene expression, but it is not clear whether this is generally true across animals. In order to understand general rules about animal clocks, and how clocks have evolved throughout Metazoa, it is necessary to study non-bilaterian animals such as cnidarians, which include corals, jellies, and sea anemones. The sea anemone Nematostella vectensis has emerged as the principal model system for cnidarian circadian biology. In this study, we show that temperature cycles entrain circadian locomotor rhythms in Nematostella, and then conduct extensive behavioral experiments across a range of light and temperature cycles to show that Nematostella's circadian behavior is disrupted by sensory conflict. Chronic exposure to conflicting light and temperature cycles also causes substantial changes to the rhythmic transcriptome, including the breakdown of rhythmic expression of various metabolic processes. These results have important implications for our understanding of cnidarian circadian clocks at both the molecular and organismal levels, and for how sensory information is processed by clocks in the absence of a central nervous system.