The objective of this study was to evaluate the impact of pH on boron, fluoride, and nitrate retention by comparing modelled speciation predictions with retention using six different nanofiltration (NF) and reverse osmosis (RO) membranes (BW30, ESPA4, NF90, TFC-S, UTC-60, and UTC-80A). Retention was explained with regard to speciation, membrane properties, and ion properties such as charge, hydrated size, and Gibbs energy of hydration. Flux was independent of pH, indicating that pH did not alter pore size and hence permeability for all membranes except UTC-60. Membrane charge (zeta potential) was strongly dependent on pH, as expected. Boron and fluoride retention depended on membrane type, pH, which correlated closely to contaminant speciation, and was due both to size and charge exclusion. While retention at low and neutral pH was a challenge for boron, high boron retention was achieved (>70% above pH 11). Fluoride retention was generally > 70% above pH 7. Nitrate retention depended on membrane, and was mostly pH independent (as was the speciation). The presence of a background electrolyte matrix (20 mM NaCl and 1 mM NaHCO3) reduced nitrate and boron retention (at high pH) due to charge shielding, and enhanced the retention of fluoride in single feed solutions, suggesting preferential transport of Cl- compared to F- with Na+.