Recruitment constraints on Singapore's dwindling fluted giant clam, Tridacna squamosa, population were studied by modelling fertilization, larval transport, and settlement using real-time hydrodynamic forcing combined with knowledge of spawning characteristics, larval development, behaviour, and settlement cues. Larval transport was simulated using a finite-volume advection-diffusion model coupled to a three-dimensional hydrodynamic model. Three recruitment constraint hypotheses were tested: 1) there is limited connectivity between Singapore's reefs and other reefs in the region, 2) there is limited exchange within Singapore's Southern Islands, and 3) there exist low-density constraints to fertilization (Allee effects). Results showed that connectivity among giant clam populations was primarily determined by residual hydrodynamic flows and spawning time, with greatest chances of successful settlement occurring when spawning and subsequent larval dispersal coincided with the period of lowest residual flow. Simulations suggested poor larval transport from reefs located along Peninsular Malaysia to Singapore, probably due to the strong surface currents between the Andaman Sea and South China Sea combined with a land barrier disrupting larval movement among reefs. The model, however, predicted offshore coral reefs to the southeast of Singapore (Bintan and Batam) may represent a significant source of larvae. Larval exchange among Singapore's Southern Islands varied substantially depending on the locations of source and sink reefs as well as spawning time; but all simulations resulted in low settler densities. Poor fertilization rates predicted by the model indicate that the low density and scattered distribution of the remaining T. squamosa in Singapore are likely to significantly inhibit any natural recovery of local stocks. © 2013 Neo et al.