Excessive growth of phytoplankton is a common and severe problem in intensively farmed pangasiid catfish (Pangasius hypophthalmus) culture ponds. It can lead to cyanobacterial blooms, reduced fish growth, bad-tasting fish flesh, and lower market demand. To investigate how to manage undesirable phytoplankton growth, we evaluated three stocking strategies in nine rural fishponds (0.020-0.022 ha) owned by various farmers: a pangasiid catfish mono culture (treatment 1, $T_1$), and pangasiid catfish-silver carp (Hypophthalmichthys molitrix) polycultures at two stocking ratios of 1:1 (treatment 2, $T_2$) and 2:1 (treatment 3, $T_3$). The total density of all ponds was approximately 30,000 fishes/ha. Monoculture ($T_1$) resulted in significantly higher (p < 0.05) nutrient levels (nitrate and phosphate) in ponds than did polyculture ($T_2$ and $T_3$). Nutrient loads increased with culture time, resulting in increased growth of phytoplankton, including Cyanophyceae (9 genera), Chlorophyceae (15 genera), Bacillariophyceae (8 genera), and Euglenophyceae (3 genera). The introduction of silver carp as a co-species helped to regulate phytoplankton growth and to improve the water quality of pangasiid catfish culture ponds.