Turbidity and sediments in hatchery ponds can adversely impact water quality and fish production. To reduce turbidity, hatchery managers use chemical coagulants, chopped hay, or cottonseed meal. However, the turbidity-causing substances removed from the water column sink to pond bottoms as sediments which, when the pond is drained, can pollute receiving water bodies. For hatcheries to operate within effluent discharge limits, total suspended solids (TSS), total settleable solids, total ammonia nitrogen, pH and carbonaceous biochemical oxygen demand (CBOD) must be effectively managed. We tested the effects of the probiotic, the Liquid Live Micro-Organisms System (LLMO), on sediment accumulation, selected water quality variables (turbidity, Secchi disk transparency, CBOD, chlorophyll a, TSS, and pH), and koi carp production in plastic-lined ponds for 148 days (June-November 2004). The LLMO was applied at 1 L per 63,237 L of pond water at two-week intervals plus a booster of the same rate applied twice weekly for six weeks toward the end of the study. Data were collected as follows: pH, daily; chlorophyll a and Secchi disk visibility, once weekly; TSS, CBOD and turbidity, 14-day intervals; and sediment and fish data, after pond draining. The results revealed no significant (P > 0.05) differences in sediment accumulation, water quality variables, and koi carp production between ponds treated with the LLMO and untreated control ponds. Our results did not support reports that LLMO can significantly reduce sludge accumulation or chlorophyll a levels, or improve water clarity.