Aberrations in blood vessel diameters can disrupt the hierarchical patterning of the vasculature and cause congenital vascular anomalies, such as arteriovenous malformations (AVMs). Despite the identification of the Bone Morphogenetic Protein (BMP) pathway as a major driver in AVM pathology, we still lack an understanding of the early embryonic events regulating vessel hierarchy and arteriovenous shunt formationin vivo. We therefore studied blood vessel diameter control of the dorsal aorta (DA) and posterior cardinal vein (PCV) in zebrafish embryos. Our findings reveal that increases in blood flow during embryonic development result in increases in arterial endothelial cell (EC) sizes, ultimately enlarging DA diameters. By contrast, anterior regions of the PCV did not respond to changes in blood flow, while caudal regions, close to the artery-vein junction, responded to changes in flow like the DA, but to a lesser extent. To unravel the mechanisms underlying the reduced response of PCV ECs to flow, we studied zebrafish embryos mutant for the BMP pathway componentsendoglinandalk1. Through the generation of genetic mosaics, we discovered that both Endoglin and Alk1 were required cell autonomously in PCV cells to restrict EC sizes and thereby limit venous diameter increases in response to flow. We further revealed that initial increases in the diameter of the caudal PCV secondarily led to increased DA diameters and cell sizes. Therefore, Alk1/Endoglin signaling prevents vein ECs from behaving like arterial ECs. This differential response of arterial and venous EC cells to increases in flow is necessary to prevent the development of AVMs. This study thus offers insights into the spatiotemporal regulation of vessel hierarchy during early development and identifies changes in EC shapes as an important contributor in determining blood vessel diameters. Failure in this mechanism underlies the vein-specific initiation of AVMs in vertebrate models of HHT.