Microcystins (MCs) produced by cyanobacteria can accumulate in freshwater fish tissues and pose potential risk to human health. In this study, variations in MC content were examined in water samples and fish tissues during a Microcystis aeruginosa-dominated bloom in a fish pond in China, from June 2009 to August 2009. A total of ten microcystin variants were detected in water samples in the fish pond, including MCLR, MCRR, MCYR, MCLF, MCLY, MCLA, and MCLW, and other three undefined MC variants. MCLR was the dominant variant in the water samples, followed by MCLF and MCLY. The highest MC concentration in the common carp (Aristichthys nobilis) was found in the order intestine > spleen > muscle; however, the order with the most MC variants detected was muscle > spleen = kidney = gallbladder > liver = intestine. The highest overall MC concentration detected in the water samples was 12.24 μg L−1, and the estimated daily intake for humans from the consumption of fish was about 0.48 μg MCLR eq kg−1 body weight (BW), 12-fold the tolerable daily intake (TDI) proposed by the World Health Organization. Therefore, the combined risks from skin exposure and food intake in this fish pond should not be overlooked.