Naturally acidic fresh waters have high conservation value, with their habitats supporting a high level of biodiversity as well as providing for rare organisms that are specially adapted to life in low-pH environments. Food webs within naturally acidic waterways are heavily reliant on the input of large amounts of organic matter from the surrounding terrestrial environment. Although these systems are found worldwide, the increasing threats of global climate change and urban developments are placing naturally acidic environments under threat of catastrophic changes to their ecology. Despite this, studies of these unique systems remain in their infancy, especially when compared with systems acidified by anthropogenic means. This paper aims to explore the varying influences on key food-web elements in naturally acidic waterways, particularly with regard to allochthonous organic matter (AOM). A conceptual model for the food webs of naturally acidic environments is presented, with the aim of providing a framework to understand the ecological functioning of these under-studied systems. This information will be critical in informing management decisions as naturally acidic streams are challenged by increasing environmental pressures. The possibility that dissolved organic carbon (DOC) can buffer organisms in naturally acidic environments against the toxicity caused by low pH is also explored.