Abstract This is the first detailed study on the occurrence of cyanobacterial toxins in India, where we studied five eutrophic, temple ponds in the vicinity of Varanasi city, Uttar Pradesh, which continuously supported blooms of Microcystis sp. for several years. Bloom material from all five ponds was sampled bi-monthly from September 2003 to August 2004. Analysis of extracts by high-performance liquid chromatography (HPLC) indicated that microcystin-RR (MC-RR) was present all year round at high concentrations (311–1540 μg/g, dry weight), posing a significant health hazard especially since all five ponds are widely used for bathing, washing, cattle drinking supply, irrigation and recreation. In addition, there was unusually low temporal variation in concentration of MC-RR in each pond, Characterization of microcystin composition of several bloom samples from this study by HPLC–PDA/MS confirmed that additional microcystins were present in many of the samples. The rarely reported, MC-AR was frequently detected in bloom samples from three of the ponds (Adityanagar, Durgakund and Sankuldhara), where it typically represented 20% of the microcystin pool. MC-WR was frequently found in samples from Adityanagar and Sankuldhara, representing 5–10% of the microcystin pool. MC-LR, along with the previously unreported MC-AHar, each represented approximately 5% of the microcystin pool when present. Bloom samples from each pond had a characteristic microcystin profile, when sampled from 2003 to 2006, suggesting persistent species/strain domination. The perennial and consistent nature of the toxic Microcystis blooms in these ponds is highly unusual, in contrast to the commonly encountered temporal and spatial variation of toxigenic and non-toxigenic species. Laboratory isolates from several ponds were shown to produce microcystins, showing similar microcystin composition to the original bloom material.