Long-term changes of fish biotic integrity in the Sanmenxia Wetland, North China, since the 1950s were assessed using the fish index of biological integrity (FIBI). The water and sediment quality was evaluated by the water quality index (WQI) and sediment pollution index (SPI). The results showed that FIBI continuously decreased from 46 to 20 during the past 5 decades, which indicated that the fish community state shifted from fair to very poor conditions, and damming by itself did not affect the fish biotic integrity. At the same time, WQI fell from 83 to 44.1, and SPI increased from 0.99 to 2.14 since the 1960s, resulting from fast regional socio-economic development and insufficient wastewater treatment. Correlation analysis suggested that water quality significantly affected biotic integrity (r = 0.867, p < 0.05) through direct effects on the fish community. As a representative example of many wetlands in North China, our study clearly demonstrated that the biological integrity was degraded, induced both by water quality deterioration and sediment pollution, further driven by the contradiction between rapid development of regional economy and lagging development of sewage treatment facilities, which were thought to be the main factor responsible for the degradation of biological integrity.