Identifying when and where environmental change induces molecular responses in natural populations is an important goal in contemporary ecology as it can aid in identifying molecular signatures of populations experiencing stressful conditions and potentially inform if species are approaching the limits of their tolerance niches. Achieving this goal is hampered by our understanding of the influence of environmental variation on the molecular systems of most ecologically relevant species as the pathways underlying fitness-affecting plastic responses have primarily been studied in model organisms under controlled laboratory conditions. To start overcoming this limitation, we establish relationships between protein abundance patterns and the abiotic environment. Profiling the proteomes of 24 natural populations of the putatively cold-adapted species Crunoecia irrorata and subsequently relating these profiles to natural variations in their abiotic freshwater spring habitats shows that protein abundances and networks respond to variation according to the functional roles these proteins have. We provide evidence that geographic and environmental distances affect protein abundances and identifications and that baseline abundances can be determined and used as information rather than noise in comparative field studies. Taking this naturally induced variation into account is a prerequisite if we are to identify the effects environmental change has on natural populations.