Abstract A systematic investigation on the role of hydrodynamics (initial permeate flux and crossflow rate) and divalent cations (calcium) in natural organic matter (NOM) fouling of nanofiltration (NF) membranes is reported. Fouling experiments with a thin-film composite NF membrane were conducted in a bench-scale, crossflow unit at various combinations of calcium ion concentration, initial permeate flux, and crossflow velocity. Results showed that membrane fouling and performance are governed by the coupled influence of chemical and hydrodynamic interactions. Permeation drag and calcium binding to NOM are the major cause for the development of a densely compacted fouling layer on the membrane surface, which leads to severe flux decline. An increase in the shear rate (crossflow velocity) mitigates these effects to some extent by reducing the accumulation of NOM on the membrane and arresting the growth of the fouling layer. The hydrodynamic and chemical interactions involved in NOM fouling are also coupled via the influence of initial permeate flux and crossflow rate on the accumulation of the rejected Ca 2+ ions near the membrane surface. At higher initial flux or low crossflow rate, the concentration of rejected Ca 2+ at the membrane surface increases due to concentration polarization, thus enhancing fouling by Ca–NOM complex and aggregate formation. The pronounced coupled influence of the initial permeate flux and crossflow velocity on the membrane fouling behavior suggests the possibility of fouling control via optimization of these parameters, thus enabling high product water flux at reduced cost.