This study determined the levels of microcystins in water and fish from Phayao Lake, Phayao Province and selected fish ponds along the Ing River tributary in Chiang Rai Province. Samples were collected monthly for 8 months (January to August 2011 for Phayao Lake, and November 2008 to June 2009 for fish ponds) and were analyzed by HPLC. The highest total microcystin-LR levels in water and fish in Phayao Lake were recorded in April 2010 at 2.60 ± 2.48 μg·L-1 and 0.20 ± 0.03 μg·kg-1 dry weight, respectively. Microcystis aeruginosa Kütz were the dominant species (271.6 ± 72.4 mm3/m3) in the lake. Colony number of Microcystis spp showed a positive correlation with soluble orthophosphate (r2 = 0.77). Similarly, Nile tilapia ponds surveyed along the tributary in Chiang Rai were contaminated with microcystins as well. The highest concentration detected in water was in March 2009 (0.58 ± 0.24 μg·L-1), whilst the maximum concentration in fish was recorded in April 2009 (2.68 ± 0.51 μg·kg-1 dry weight). Microcystis spp. dominated the pond waters and was positively correlated with chlorophyll a (r2=0.80) and soluble nitrate (r2=0.71). The highest concentration of the cyanobacteria was recorded in February 2009 at 4272.5 ± 62.3 mm3/m3. Results showed that total microcystin-LR concentration in fish in Chiang Rai ponds were higher than in Phayao Lake. This study suggested the possible health risks associated with the bioaccumulation of microcystins in fish (Nile tilapia) cultivated in fish ponds along the tributary in Chiang Rai and in Phayao Lake.