Biodiversity loss is one of the major threats to humanity. This has led to an increasing amount of research on biodiversity on genetic and species levels. Studies of diversity at the ecosystem level has however been neglected. An important aspect of ecosystems is food webs that describe the predation-prey interactions between species. Properties explaining the topological structure of food webs can be used to compare and highlight differences between ecosystems. In the present study, topological network properties are used to compare the diversity of network structures between groups of empirical food webs. Differences between 45 aquatic and 45 terrestrial food webs are compared as well as the effects of species richness on lake network structure diversity. Network structure diversity is measured as the average Euclidean distance from food webs to their group centroid in a multidimensional space of network properties. While the average network structure differs between aquatic and terrestrial food webs, no significant difference in variation is found. For 128 Swedish and 48 North American lake food webs, increasing species richness is shown to decrease network structure diversity. A higher diversity of network structures could potentially indicate a more ways to cope with disturbances or provisions of a higher variety of ecosystem services. Preliminary tests of ecosystem diversity effects on stability were conducted but proved inconclusive.