This dataset record provides deposition values of sulphur and nitrogen deposition and concentration values for ammonia (NH3), sulphur dioxide (SO2) and nitrogen oxide (NOx) on the UK nature conservation protected sites, averaged over the years 2014 to 2016. The set also includes calculated minimum, maximum and gridded average values for each site. Protected nature sites covered are: (i) Special Areas of Conservation (SAC) (ii) Special Protection Areas (SPA) (iii) Sites of Special Scientific Interest (SSSI). The data consist of values of nitrogen and acid deposition, and concentrations of ammonia (NH3) based on the Concentration Based Estimated Deposition (CBED), and concentrations of NOx and SO2 using the Pollution Climate Mapping (PCM) model. Nitrogen and acid deposition data is also given for specific habitat types including: (i) moorland/short vegetation everywhere, (ii) forest everywhere, and (iii) the grid square average over multiple land cover types (i.e. arable, grassland, forest, moorland, urban) These habitat-specific data are recommended for use with critical loads and levels for the calculation of critical load/level exceedances using the relevant habitat type. Full details about this dataset can be found at https://doi.org/10.5285/735dd995-333c-4b02-8fb1-287b7b2cefdf