Capping water body sediments with a thin layer of sand is an effective technique to decrease nutrient concentrations in the water column and accelerate ecological restoration of eutrophic water bodies. However, long-term effects of thin-layer sand capping in shallow lakes are reported less often. Using clean fine sand and geotextile mats as capping materials for sediments collected from Wuhan Donghu Lake in China, we designed a 290-day tank experiment with 3 cm of sand capping at four percentages of sediment coverage from 25 to 100% and a control (no capping). We monitored total nitrogen (TN), total phosphorus (TP), nitrate (NO3-), ammonia (NH4+), and soluble reactive phosphorus (SRP) in the overlying water every 7 days. Mean TN and NO3- concentrations were significantly the lowest (P < 0.05) at 50% coverage. Further increase in coverage kept them slightly fluctuating. NH4+ concentration was significantly lowest (P < 0.05) at 75% coverage. The relation between coverage and mean TP and SRP concentrations indicated that 75% coverage significantly decreased (P < 0.05) them, and increasing coverage to 100% decreased them even more. The fluxes of TN and TP estimated between sediments and overlying water showed that the thin fine-sand layer significantly increased the function of sediments as a sink of TN from overlying water and the potential of a sand layer to block release of TP from sediments (P < 0.05). Our results suggested that if thin-layer sand capping were applied to Wuhan Donghu Lake, more than 50% coverage is required to decrease nutrients in the lake's water.