Abstract We present and analyze an a posteriori error estimator based on mesh refinement for the solution of the hypersingular boundary integral equation governing the Laplacian in three dimensions. The discretization under consideration is a nonconforming domain decomposition method based on the Nitsche technique. Assuming a saturation property, we establish quasireliability and efficiency of the error estimator in comparison with the error in a natural (nonconforming) norm. Numerical experiments with uniform and adaptively refined meshes confirm our theoretical results. © 2013 Wiley Periodicals, Inc. Numer Methods Partial Differential Eq 30: 947–963, 2014