The results of an analysis of the connectivity of sixteen priority habitat networks in England using the Condatis methodology. The dataset includes conductance scores for each of the priority habitat networks (an overall assessment of how connected the habitat network is), the flow scores for each contiguous habitat patch within each of the habitat networks (the importance of that patch to connectivity), as well as details of protection. Additionally, the dataset includes data and scripts needed to run a demonstration Condatis analysis, and produced the figures used in Travers et al., 2021 (in prep.). Dispersal distances of 2, 4 and 8 km were used as inputs into Condatis. The outputs of connectivity assessments using those dispersal figures were geometrically averaged to provide results summing up the connectedness of a habitat network over a range of dispersal abilities. To determine how much connectivity (flow), and which patches were protected in each habitat network they were overlaid with SSSI and NNR spatial data. If more than 50% of a patch’s area was covered by a protected area it was determined to be protected. Full details about this dataset can be found at https://doi.org/10.5285/a715112e-08ae-4d6e-943a-77933fd5ddd1