Three selected mussel tissues (digestive gland, mantle, and gills) were studied to determine which was the most suitable for the potential use of the cellular energy allocation (CEA) methodology in indigenous mussels Mytilus galloprovincialis. In addition, the applicability of CEA in the assessment of natural stress caused by salinity fluctuations in stratified estuary was tested in selected tissues. It was important to identify the mussel gender to reliably assess the changes in organism energy budget. CEA value was calculated as a ratio between available energy (E_a) and energy consumption (E_c). Mantle tissue was under the strongest influence of the differences in protein and lipid content between male and female mussels, and therefore reflected physiological changes in the organism itself, rather than those caused by natural environmental stress. CEA in gills had lower values than in mantle and digestive gland, and was similar at two selected sampling sites, so the changes in CEA caused by natural stress could not be detected in the gill tissue. Greater E_c in mussels from the estuarine site than from the coastal site was detected only in the digestive gland tissue, and can probably be attributed to the energetically costly maintenance of osmotic balance. Last, using digestive gland tissue in CEA analysis demonstrated a clear difference between coastal and estuarine sampling sites, providing the measure of the natural stress posed by variations in salinity.