Inorganic contamination in drinking water, especially fluoride and uranium, has been recognized as a worldwide problem imposing a serious threat to human health. Among several treatment technologies applied for fluoride and uranium removal, nanofiltration (NF) and reverse osmosis (RO) have been studied extensively and proven to offer satisfactory results with high selectivity. In this review, a comprehensive summary and critical analysis of previous NF and RO applications on fluoride and uranium removal is presented. Fluoride retention is generally governed by size exclusion and charge interaction, while uranium retention is strongly affected by the speciation of uranium and size exclusion usually plays a predominant role for all species. Adsorption on the membrane occurs as some uranium species interact with membrane functional groups. The influence of operating conditions (pressure, crossflow velocity), water quality (concentration, solution pH), solute–solute interactions, membrane characteristics and membrane fouling on fluoride and uranium retention is critically reviewed.