This study uses morphometric analysis for better understanding processes occurring during the spawning period in the population of threespine stickleback Gasterosteus aculeatus. Totally, 270 specimens were sampled in 2016 in the Keret Archipelago (White Sea) from three spawning grounds of different quality in the beginning (28–30 May), middle (15–17 June) and end (7–9 July) of spawning period. Nine characters describing fish body shape were measured on each specimen using scanned image and caliper: 1) Total Length, 2) Standard Length, 3) Head Length, 4) Maxilla Length, 5) Distance Between Head and Pectoral Fin, 6) Body Depth, 7) Body Thickness, 8) Head Thickness, 9) Caudal Length. For analyses, we used ratio of characters 3–9 to Standard Length. Principal Component Analysis has separated several groups of characters, describing the upper part of the body (Characters 3–5), body volume (Characters 6–8), and Caudal Length (9). Separation of the groups was similar in both sexes. All groups of characters showed notable changes during the spawning period. In the beginning, the spatial heterogeneity of samples was low, meaning that in wintering locations the population is not structured. In the middle of spawning season, the highest heterogeneity was observed. Males characterized by larger upper part of the body and larger size, were numerous in high quality spawning grounds (characterized by high density of sea grass and stickleback). This probably results from a competition between territorial males for higher quality spawning grounds. In the end of spawning period no spatial heterogeneity was observed, probably, because most of stickleback left the spawning grounds and no competition for higher quality spawning grounds took place. Spatial heterogeneity was somewhat lower in females, but also statistically significant in several cases. Group of characters describing body volume, in general, showed the decline during the spawning period, reflecting release of eggs in females and loss of energy associated with spawning (more pronounced in males guarding their progeny). Superimposition of several processes, such as competition for fish for better spawning grounds, release of eggs and loss of energy associated with spawning, and inshore and offshore migrations, results in a dynamic and complicated picture of morphological heterogeneity occurring during the spawning season of the threespine stickleback.