Purpose: Despite advances in 3D surgical scene understanding, semantic simultaneous localisation and mapping (SLAM) remains under-explored for two key reasons. First, it requires solving three challenging tasks in parallel: camera pose tracking, high-fidelity deformable reconstruction, and semantic mapping, making progress particularly demanding. Second, the scarcity of datasets providing the necessary ground truth to evaluate all three tasks comprehensively under conditions that closely reflect real surgical procedures environments. Method: We propose EndoS3, a Gaussian Splatting-based semantic SLAM framework that uses instance masks to guide all three tasks. An instance-level motion decomposition module separates static and dynamic instances by evaluating residual flow after compensating for camera motion, accounting for flow noise and comparing motion across neighbouring instances. The camera is tracked against the static Gaussians, while an instance-aware warp field gives each dynamic instance its own control nodes and deformation network. A semantic node allocation module redistributes a fixed node budget across instances according to their size and non-rigidity. We also introduce CRCD++, an ex-vivo Cholecystectomy dataset with RGB-D frames, camera pose and instance annotations for full semantic SLAM evaluation. Results: EndoS3 surpasses all state-of-the-art general-purpose and surgical semantic SLAM methods in tracking, reconstruction and semantic mapping on the CRCD++ and SemSup datasets. Conclusion: Semantic-aware motion and deformation modelling is vital to surgical semantic SLAM. EndoS3 and CRCD++ offer a method and benchmark for improved geometric and semantic understanding in endoscopy.

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