The impact of pH and humic acid (HA) on the retention of fluoride (F) and inorganic carbon (IC) by nanofiltration (NF) and reverse osmosis (RO) membranes was determined. Synthetic waters were prepared using realistic ranges of F, IC and HA for carbonaceous waters found for example in the fluoride rich waters in Tanzania. These waters were filtered using NF270 and BW30 membranes to determine retention mechanisms. IC changes speciation with pH. The dominant species at pH < 6, 6-10 and > 10 are H2CO3, HCO3 and CO32- respectively. This results in changes in charge and size of the hydrated ion radius. The mechanism for IC retention by the NF270 and BW30 membranes are charge repulsion and size exclusion, respectively. F retention increases with pH. IC influenced F retention at pH > 10 where IC exists as divalent CO32- and is retained more easily than the monovalent F. HA enhances the retention of F by NF/RO membranes under certain conditions. The enhancement effect is more pronounced at neutral than at acidic pH and basic pH. The mechanism for the enhancement is attributed to the change in surface charge of the membranes by adsorption of HA. At high HA concentration the F retention enhancement is annulled by deposit formation on the membrane. The results obtained in this study indicate the complexity of retention in real surface- and ground waters that can alter significantly in pH as well as IC and HA content. The research is situated in the context of developing membrane technologies for autonomous systems in remote locations where water quality is variable and mechanisms of membrane performance are poorly understood.