The present paper dealt with the impacts of water level fluctuations on the lakeshore substrate environments of the shallow lakes in the middle and lower reaches of the Yangtze River. The results showed that substrate environments changed greatly with the elevation gradients. Moisture contents of substrate decreased as the elevation increased, and pH value changed little, while contents of organic matter, total nitrogen and total phosphorus in substrate increased at first and then decreased. Also, substrate environments showed clear seasonal dynamics. Analyses showed that the amplitude of water level fluctuations, submergence depth, and duration of high water level had great impacts on the substrates. The coefficients of variation of substrate parameters were the largest in the medium amplitude, indicating that the highest heterogeneity of substrate occurred under such a condition. Substrate nutrients would be lost at an increasing pace with the increase of time and depth submerged during summer. If the duration of high water level was long, the pH values would be changed greater and the nutrients would be lost faster. Our results offered a scientific foundation for ecological restoration and management of the lakeshore.