An 8 month investigation into the quality of water from open and rope-pump shallow wells in rural Cambodia was conducted. Wells were analysed for indicators of the health (arsenic, fluoride, manganese, nitrate, total coliforms, E. coli, male-specific coliphage) and aesthetic (iron, chloride, conductivity, total dissolved solids, hardnesss, turbidity, pH) quality of the water, and referenced to the Cambodian Drinking Water Standard when available. The shallow aquifer was chemically less of a health risk than the deep aquifer; however, microbial contamination was considerable for both shallow well types with mean E. coli loads of 103 CFU/100 mL and male-specific coliphage contamination of 102 PFU/eluate. Temporal variation in microbial contamination was significant (p < 0.05), with overall loads decreasing during the dry season. The aesthetic quality of the water was poor for all samples, but worsened during the dry season. No significant difference was observed in the quality of water from open and rope-pump wells, despite their classification as unimproved and improved respectively by the WHO/UNICEF Joint Monitoring Programme. Contaminants present in both well types may readily be removed by simple water treatment, suggesting that household treatment may be more beneficial to rural Cambodian households than shallow aquifer source improvements.