Estuaries are special geographical units of sea and land alternation, and are sensitive to changes in environmental factors. Zostera japonica is a very widespread seagrass species in the Yellow River Estuary, China and seagrass beds consisted of them are important estuary ecosystem resources. Water and sediment regulation at the Xiaolangdi Reservoir on the Yellow River can change the water environment in the estuary and threaten seagrass distribution. We evaluated the salinity and turbidity stress on Z. japonica by site sampling and laboratory tests, and compared both sets of growth conditions. We then set turbidity and salinity gradients to quantify the variation in sediment and salinity conditions imposed by the water and sediment regulation. Results showed that changes in Z. japonica biomass can be used as a stress indicator. Salinity levels of 20 ppt and turbidity levels below 50 NTU were the most suitable for growth. Biomass decreased as turbidity increased. At high turbidity (> 100 NTU), growth in low salinity (< 20 ppt) was significantly better than at high salinity (> 25 ppt). The rank of inhibitory effect of salinity, turbidity and interactive salinity–turbidity treatment on the juvenile stage was salinity > salinity–turbidity interaction > turbidity. The rank of inhibitory effect on the mature stage was turbidity > salinity–turbidity interaction > salinity. Salinity inhibited growth at the juvenile stage, while turbidity inhibited growth at the mature stage. Our research suggested that Z. japonica can adapt to resist the stress of changing salinity and turbidity, and this has great significance to the sustainability of the seagrass bed in the Yellow River Estuary.