Bivalves’ physiological functions (i.e. growth, reproduction) are influenced by environmental variability that can be concomitant with trophic resource variations in terms of quality and quantity. Among the essential molecules that bivalves need to acquire from their diet to maintain physiological functions, fatty acids (FAs) such as polyunsaturated fatty acids (e.g. 20:4n-6 (arachidonic acid), 20:5n-3 (eicosapentaenoic acid) and 22:6n-3 (docosahexaenoic acid)) have been described to play a critical role. The present study examined the FA composition of gill membrane lipids of two bivalve species, Nodipecten subnodosus and Spondylus crassisquama, sampled in a coastal lagoon of the Northeastern Pacific (Ojo de Liebre, Mexico), at two contrasting locations (inner versus outer part of the lagoon) and at two different periods (February and August 2016). Spatiotemporal variations showed that FA composition of gill membrane lipids was highly correlated to FA composition of reserve lipids from digestive gland. This highlights the marked impact of the diet on FA composition of gill membranes. Interestingly, both species presented differences in the seasonal accumulations of plasmalogens and of particular FA that are not found in their diet (e.g. non-methylene interrupted FA, 22:4n-9trans, 20:1n-11), suggesting specific regulations of FA incorporation and lipid class composition in gill membranes to maintain optimal membrane function in their specific and changing environment. This study highlights the importance to characterize the spatial and temporal variability of food resources in order to apprehend the physiological consequences of environmental variability, as well as species differential regulation capacities in a changing world.