Sustaining good water quality in aquaculture ponds is vital. Without an aerator, the dissolved oxygen in ponds comes primarily from mass transfer at the water-ambient atmosphere interface. As sediment can seriously affect water quality, this study used indoor experiments to examine the nutrient (nitrogen and phosphorus) release mechanisms and fluxes from sediment in aquaculture ponds with moving water but no aeration. The results showed that the ammonia nitrogen (NH3-N) concentration in the overlying water was inversely proportional to flow velocity and that a higher flow velocity tended to result in a lower concentration in the overlying water, a steeper vertical gradient of concentration within the bed sediments, and a faster release rate from the sediments. The sediment disturbed by flowing water released more nitrate nitrogen (NO3-N) and nitrite nitrogen (NO2-N) into the overlying water and NO2-N could become oxidized into NO3-N. In still water, NO3-N was released gradually and some anaerobic NO3-N was nitrified into NO2-N. Phosphorus release from the sediments was controlled by the adsorption–desorption balance, with the phosphorus concentration in the overlying water dropping gradually to a steady value from its initial maximum. The relationship between NH3-N release flux and flow rate is described by a cubic function.