Non-additive interactions between environmental stressors, where responses to simultaneous stressors do not equal the sum of individual-stressor responses, commonly occur across organisms and environments. To enable predictions of organismal resilience to shifting patterns of environmental stressors, it is important to both identify these interactions and document the mechanisms underlying them. The supratidal copepod Tigriopus californicus demonstrates a non-additive, antagonistic pattern of increased heat tolerance when simultaneously exposed to high salinities. We investigated salinity’s chronic and acute effects on heat tolerance in a northern population and then quantified responses in protein abundance to hypersalinity and heat stress, both alone and in combination. The overall proteomic response to multiple stressors was non-additive and largely reflected that to high temperature. However, 42% of multi-stressor proteins were absent from either single-stressor response; we refer to these proteins that are only differentially abundant in the multi-stressor scenario as “emergent”. Our results suggest that the increased heat tolerance of T. californicus conferred by hypersalinity may be driven by a combination of these emergent proteins, several proteins induced by hypersalinity in both single- and multi-stressor conditions that may contribute to cross-tolerance, and four proteins with additive abundance patterns (including a small heat shock protein). These candidate proteins play putative roles in several relevant processes including the heat shock response, protein folding, regulation of metabolism, and mitigation of oxidative stress. Our results connect to prior findings in whole organisms and highlight promising pathways for future investigation in the context of heat tolerance and multi-stressor interactions.