BACKGROUND & OBJECTIVES: Selected physico-chemical characteristics of flowing and pooled water in a stream that generated two malaria vectors, Anopheles culicifacies s.l. Giles and Anopheles varuna Iyengar, were investigated during August-September 1997 and July 1998 at the Upper Yan Oya watershed in north-central Sri Lanka. METHODS: The physico-chemical parameters measured were: temperature, dissolved oxygen, pH, conductivity, total dissolved solids, alkalinity, ammonia nitrogen, nitrate nitrogen, calcium, magnesium, carbondioxide, ferrous iron, phosphate, colour and turbidity. In total, 75.5% of 151 samples analysed were mosquito-positive. Logistic regression was used for statistical analysis. RESULTS: Among physico-chemical parameters, An. culicifacies (the major malaria vector in the country) was positively related only to temperature, and An. varuna (a secondary malaria vector) to calcium. Among habitat characteristics, An. culicifacies was associated with light and vegetation, and negatively associated with the presence of potential predators. An. varuna was positively associated with other aquatic fauna. INTERPRETATION & CONCLUSION: Surprisingly this detailed study did not find an association between An. culicifacies and dissolved oxygen as previously found in the few studies that have looked at physico-chemical characteristics of malaria vector breeding habitats in south Asia. This study, along with existing information from other studies indicate that most of the physico-chemical parameters measured under natural conditions within the same habitat type is insufficient to explain the distribution of vectors within such habitats. However, it seems likely that both An. culicifacies and An. varuna follow a strategy whereby ovipositing females scatter their eggs over most of or all of a highly temporary and only transiently available stream bed pool habitat, in order to optimise breeding success.