In Bangladesh the exposure of millions of inhabitants to water from (shallow) tube wells contaminated with high geogenic loads of arsenic is a major concern. As an alternative to the costly drilling of deep wells, the return to the use of surface water as a source of drinking water is considered. In addition to the well-known hazards of water borne infectious diseases associated with the use of surface water, recently the potential public health implications of toxic cyanobacteria have been recognized. As a first step towards a risk assessment for cyanotoxins in Bangladesh surface waters, seston samples of 79 ponds were analysed in late summer 2002 for the presence of cyanobacteria and microcystins (MCYST), the most frequently detected cyanobacterial toxins worldwide. Microcystins could be detected in 39 ponds, mostly together with varying abundance of potentially microcystin-producing genera such as Microcystis, Planktothrix and Anabaena. Total microcystin concentrations ranged between <0.1 and >1,000 μg l−1, and more than half of the positive samples contained high concentrations of more than 10 μg l−1. The results clearly show that concentrations of microcystins well above the provisional WHO guideline value of 1 μg l−1 MCYST-LR can be frequently detected in Bangladesh ponds. Thus, an increasing use of surface water for human consumption introduces a risk of replacing one health hazard by another and therefore needs to be accompanied by cyanotoxin hazard assessments.