Removal of boron from saline water sources has presented a major challenge for commercially available reverse osmosis desalination membranes. In this work, we report the boron and sodium chloride separation properties of truly defect-free, highly selective, interfacially polymerized aromatic polyamide thin-film composite membranes. The fabricated membranes show potential for separating sodium chloride with a maximum rejection of 99.6% obtained for the optimized film-forming protocol under lab-scale brackish water desalination conditions. This translated into promising boron rejection performance with rejections of up to 99% at pH 10, higher than a number of commercially available reverse osmosis membranes tested in-house. Comprehensive characterization including X-ray photoelectron spectroscopy, atomic force microscopy, scanning electron microscopy, ellipsometry, and surface charge measurements revealed intimate insights on interfacially polymerized polyamide membrane structure-property relationships. Increased membrane crosslinking was shown to be the primary determining factor for membrane permselectivity performance. Furthermore, relationships were established between microstructural properties such as crosslinking and morphological characteristics like surface roughness, highlighting an intricate and complex structure formation mechanism.