Connectivity in pond ecosystems is essential for amphibian population persistence. To test the role of connectivity, a diversity of scales accounting for the different processes underlying species distribution needs to be considered. Several approaches exist for accounting for the potential connectivity, mainly based on structural versus functional methods. Based on occupancy data, our aim was to assess the relative power of connectivity metrics in explaining amphibian distribution when accounting for cross‐scale effects from pond to network scales, and to identify network features relevant to amphibian conservation in agricultural landscapes in the Seine‐et‐Marne department (east of Paris, France). We propose an original analytical framework that allows examining different spatial scales of influence, with a focus on connectivity. We analyse the distribution of three amphibian species ( Bufo bufo , Rana dalmatina , and Lissotriton vulgaris ) in relation to various pond conditions (fish presence, water quality, and nearby woodland habitat) as well as connectivity using three connectivity approaches: (1) structural, (2) area‐functional based on potential migration areas, and (3) path‐functional based on the least accumulated cost paths. Values of landscape resistance were assigned according to a biological risk‐based approach that is proposed as an enhanced, transparent expert‐based approach. We further investigated cross‐scale effects in amphibian responses to the environment by assessing the relative importance of pond and network characteristics as well as their interactions. Despite some species‐specific characteristics, the area‐functional approach of connectivity was generally the most effective in explaining species distribution by emphasising the relevance of potential migration areas as conservation units. Although pond conditions usually had a greater influence than network connectivity, we highlighted important cross‐scale and threshold effects in species’ response to local conditions, to pond connectivity, and to the availability of potentially suitable terrestrial habitats in the networks. Our cross‐scale approach accounts for scale‐dependent processes that potentially underlie amphibian distribution such as habitat selection and metapopulation dynamics. Both structural and functional connectivity should be considered as complementary features of pond connectivity when dispersal traits are likely to be less limiting. From a management perspective, our results encourage conservation plans to combine functional network‐centred strategies with the preservation of local conditions. We give guidelines as to the features of such networks to help maintain amphibian populations in agricultural landscapes.