Understanding the extrinsic factors that drive the emergence of biological diversity is critical to its protection and management. However, even superficially similar local environments can vary considerably, and so large-scale datasets are needed to understand the key drivers across a representative portion of a species distribution. Arctic charr (Salvelinus alpinus) is a widespread salmonid fish that represents an excellent study system for these processes because the species shows substantial diversification to a range of freshwater environments and multiple instances of trophic specialisation in the form of sympatric ecotype populations. However, the processes behind this variation remain largely unknown due to a lack of broad-scale studies. To address this, we investigated the drivers of diversity using a national scale study of 64 Arctic charr populations in lakes across Scotland using a genome-wide dataset of SNPs (N = 24,878) and phenotypic data of head depth relative to body size. We found that the extent of genetic and phenotypic diversity was predicted by ecosystem size (a proxy of lake size, depth and complexity). We suggest this is because larger, deeper lakes generally provided more ecological opportunity and diversification potential. Additionally, using environmental data from all 187 lakes containing Arctic charr in Scotland, we found that ecosystem size strongly predicted the potential for trophic specialisation and the presence of sympatric divergent ecotypes. Our results show the importance of ecological opportunity in underlying adaptive radiations