The presence of omnivorous fish is known to affect aquatic ecosystems, including water quality. The effect, however, depends on the species in question, and our knowledge is limited on the effect of omnivorous crucian carp (Carassius auratus), a common and often the most numerous fish species in eutrophic shallow lakes in China. We conducted a 70-day outdoor experiment in mesocosms with and without crucian carp to examine whether this species adversely affects water quality by increasing the levels of total nitrogen (TN) and total phosphorus (TP), thereby stimulating the biomass of phytoplankton and increasing water turbidity. Compared with carp-free controls, the presence of crucian carp resulted in higher TN and TP in the water column, greater phytoplankton biomass and lower periphyton biomass, measured as chlorophyll a. Total suspended solids (TSS) also increased in the presence of fish. We conclude that crucian carp can increase TN and TP, enhance phytoplankton biomass, and increase water turbidity, thereby contributing significantly to the deterioration of the water quality. In addition to controlling external nutrient loading, the removal of crucian carp may help to improve water quality in warm shallow eutrophic lakes.