Spatially balanced sampling designs, such as the local pivotal methods (LPM), improve representation of auxiliary-variable space, but design-based variance estimation is challenging because second-order inclusion probabilities are generally intractable and may be zero or near zero. We propose two approaches for estimating the variance of the Horvitz-Thompson mean and the finite-population variance. The first estimates joint inclusion probabilities by Monte Carlo simulation and uses pairwise independence tests to modify the resulting variance estimators. The second, a model-assisted bootstrap (MABS), uses an interpolating Gaussian process to construct a synthetic finite population and estimates variance by resampling under the original LPM design. In simulations, the modified empirical approach performs well when responses are strongly associated with auxiliary variables, but its performance for the Horvitz-Thompson mean deteriorates as this association weakens. MABS exhibits more stable performance across noise levels and sampling settings, including under LPM2 and non-Gaussian noise. For finite-population variance estimation, however, no method shows a uniform advantage. These results illustrate the complementary strengths of the proposed approaches for inference under spatially balanced sampling.

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