Threespine stickleback Gasterosteus aculeatus of theWhite Sea perform spawning migrations from the wintering areas to the inshore zone in early summer. To describe the spatial heterogeneity of the spawning agglomerations of stickleback, we compared size characteristics and biochemical parameters in different organs of spawners from three locations of theKandalakshaBay. The sampling locations are situated within a few kilometers from each other but notably differing in temperature regime, feeding resources, and underwater vegetation. The samples have been collected within a week after appearance of fish in the inshore zone. We did not find differences between samples by size characteristics. The activity of intracellular calcium-dependent proteases (calpains) significantly differed in fish from different samples. The results obtained can be explained by both the initial genetic differences of fish from different spawning grounds or the response of initially homogeneous groups of sticklebacks to different environmental conditions. The first explanation is supported by the fact that quite long time of living in new conditions is required to result in differences in calpain activity, and the time, which passed after the separation of spawners in our sampling locations is likely not sufficient for such differentiation. The second explanation is supported by studies of winter distribution of stickleback in the area showing that the wintering areas are quite far from the inshore zone and mixing in wintering locations preventing population structuring can be supposed. Moreover, the patterns of calpain activity are more similar in fish caught under more similar conditions, which may indicate environmental reasons of the observed biochemical differences. By the moment, we have no reason to prefer one explanation to another. For that, it is needed to perform studies on size and biochemical distribution of stickleback at later stages of the spawning.