The context and cause of adaptive radiations has been widely described and explored but why rapid evolutionary diversification does not occur in related evolutionary lineages has yet to be understood. One possible answer to this is simply that evolutionary diversification is provoked by environmental diversity, and that some lineages do not encounter the necessary environmental diversity. Three-spined stickleback on the Scottish island of North Uist show enormous diversification, which seems to be associated with the diversity of aquatic habitats. Stickleback on the neighbouring island of South Uist have not been reported to show the same level of evolutionary diversity, despite levels of environmental variation that we might expect to be similar to North Uist. In this study, we compared patterns of morphological and environmental diversity on North and South Uist. Ancestral anadromous stickleback from both islands exhibited similar morphology including size and bony ‘armour’. Resident stickleback showed significant variation in armour traits in relation to pH of water. However, North Uist stickleback exhibited greater diversity of morphological traits than South Uist and this was associated with greater diversity in pH of the waters of lochs on North Uist. Highly acidic and highly alkaline freshwater habitats are missing, or uncommon, on South Uist. Thus, pH appears to act as a causal factor driving the evolutionary diversification of stickleback in local adaptation in North and South Uist. This is consistent with diversification being more associated with ecological constraint than ecological opportunity.