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Two-dimensional (2D) materials are increasingly being used as active components in nanoscale devices. Many interesting properties of 2D materials stem from the reduced and highly non-local electronic screening in two dimensions. While electronic screening within 2D materials has been studied extensively, the question still remains of how 2D substrates screen charge perturbations or electronic excitations adjacent to them. Thickness-dependent dielectric screening properties have recently been studied using electrostatic force microscopy (EFM) experiments. However, it was suggested that some of the thickness-dependent trends were due to extrinsic effects. Similarly, Kelvin probe measurements (KPM) indicate that charge fluctuations are reduced when BN slabs are placed on SiO$_2$, but it is unclear if this effect is due to intrinsic screening from BN. In this work, we use first principles calculations to study the fully non-local dielectric screening properties of 2D material substrates. Our simulations give results in good qualitative agreement with those from EFM experiments, for hexagonal boron nitride (BN), graphene and MoS$_2$, indicating that the experimentally observed thickness-dependent screening effects are intrinsic to the 2D materials. We further investigate explicitly the role of BN in lowering charge potential fluctuations arising from charge impurities on an underlying SiO$_2$ substrate, as observed in the KPM experiments. 2D material substrates can also dramatically change the HOMO-LUMO gaps of adsorbates, especially for small molecules, such as benzene. We propose a reliable and very quick method to predict the HOMO-LUMO gap of small physisorbed molecules on 2D and 3D substrates, using only the band gap of the substrate and the gas phase gap of the molecule.