Carboxyls are inherent functional groups of thin-film composite polyamide nanofiltration (NF) membranes, which may play a role in membrane performance and fouling. Their surface presence is attributed to incomplete reaction of acyl chloride monomers during the membrane active layer synthesis by interfacial polymerization. In order to unravel the effect of carboxyl group density on organic fouling, NF membranes were fabricated by reacting piperazine (PIP) with either isophthaloyl chloride (IPC) or the more commonly used trimesoyl chloride (TMC). Fouling experiments were conducted with alginate as a model hydrophilic organic foulant in a solution, simulating the composition of municipal secondary effluent. Improved antifouling properties were observed for the IPC membrane, which exhibited lower flux decline (40%) and significantly greater fouling reversibility or cleaning efficiency (74%) than the TMC membrane (51% flux decline and 40% cleaning efficiency). Surface characterization revealed that there was a substantial difference in the density of surface carboxyl groups between the IPC and TMC membranes, while other surface properties were comparable. The role of carboxyl groups was elucidated by measurements of foulant-surface intermolecular forces by atomic force microscopy, which showed lower adhesion forces and rupture distances for the IPC membrane compared to TMC membranes in the presence of calcium ions in solution. Our results demonstrated that a decrease in surface carboxyl group density of polyamide membranes fabricated with IPC monomers can prevent calcium bridging with alginate and, thus, improve membrane antifouling properties.