A method for securing data stream processing includes implementing a stage of a data processing pipeline in a trusted execution environment. A state of the stage is represented by a graph-based data structure. Protected memory of the trusted execution environment is reserved for computations of the stage. A key-value store is maintained in the protected memory. The key-value store includes hashes of graph segments of the graph-based data structure for the computations and memory locations of the graph segments. A state part of the computations is moved from the protected memory to unprotected memory. The state part of the computations is loaded back to the protected memory. An integrity of a computation using the state part of the computations is checked using the hashes in the key-value store.