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Abstract Climate change is raising sea levels across the globe. On river deltas, sea‐level rise (SLR) may result in land loss, saline intrusion into groundwater aquifers, and other problems that adversely impact coastal communities. There is significant uncertainty surrounding future SLR trajectories and magnitudes, even over decadal timescales. Given this uncertainty, numerical modeling is needed to explore how different SLR projections may impact river delta evolution. In this work, we apply the pyDeltaRCM numerical model to simulate 350 years of deltaic evolution under three different SLR trajectories: steady rise, an abrupt change in SLR rate, and a gradual acceleration of SLR. For each SLR trajectory, we test a set of six final SLR magnitudes between 5 and 40 mm/yr, in addition to control runs with no SLR. We find that both surface channel dynamics as well as aspects of the subsurface change in response to higher rates of SLR, even over centennial timescales. In particular, increased channel mobility due to SLR corresponds to higher sand connectivity in the subsurface. Both the trajectory and magnitude of SLR change influence the evolution of the delta surface, which in turn modifies the structure of the subsurface. We identify correlations between surface and subsurface properties, and find that inferences of subsurface structure from the current surface configuration should be limited to time spans over which the sea level forcing is approximately steady. As a result, this work improves our ability to predict future delta evolution and subsurface connectivity as sea levels continue to rise.