In order to provide safe drinking water in isolated communities where water supply and electrical infrastructure is limited, a system combining solar energy and advanced water treatment technology (a two-staged membrane process with ultrafiltration followed by nanofiltration/reverse osmosis (NF/RO)) has been developed. The objective of this study is to model the speciation of commonly-occurring and sometimes health-threatening trace contaminants, and then to evaluate the impact of speciation on fluoride, arsenic, and magnesium retention by NF/RO. A series of experiments were performed in central Australia in late 2005 to assess elemental retention with four different membrane modules (BW30, ESPA4, NF90, and TFC-S) at various pH values between 3 and 11 at two different source waters (Pine Hill Station and Ti Tree Farm). The removal of fluoride and arsenic was observed to be independent of pH, while magnesium removal is pH dependent. Compound speciation is considered to explain dependence observations. Membrane type was found to impact retention. The results obtained in this study will provide valuable information on the reliability and the optimization windows of the renewable energy powered desalination system that has been developed.