Mesolithic harpoons are structurally complex weapon points and significant sources of archaeological information. Nonetheless, separating different types of information inherent in harpoon point shapes (e.g., aspects relating to mechanical performance, personal or group craft variation and chronology) using descriptive approaches is difficult. In this study, we employed an exploratory geometric morphometric approach to the analysis of 28 Mesolithic harpoon points, and 144 undated harpoon points from the circum-Baltic Sea area in order to retrieve both functional and spatiotemporal information. By analyzing harpoon structure statistically through (i.) a shape proxy (harpoon silhouette) and (ii.) harpoon sub-structures (barbs), we have been able to reveal information related to both variation in shape convention and functional constraints. Barb shape results revealed statistically significant chronological and geographical groupings with spatiotemporal barb-shape trajectories made visible and objective evaluation of how barb-shape conventions impacted functional variation. In addition, harpoon silhouette shape distributions were shown to have potential as sources for robust artifact classifications in relation to functional constraints and raw-material engagement. These results suggest that morphometric approaches similar to the ones we have employed offer promising ways of addressing specific archaeological questions in the context of harpoon point shapes and, more generally, other complex weapon point forms.