We describe an approach to assessing biological health in a heavily utilized, large lowland river setting, using the example of the lower Yellow River, China. In this study, the river was divided into four reaches, and a field survey of fish, benthic macroinvertebrates, and riparian plants was undertaken. Data from historical records were used for reference. The scoring system used weighting to adjust for differences in the importance of the chosen indicators and the relative efficiency of the sampling effort. The results indicated that the biological health of the lower Yellow River is distant from historical reference conditions, with its condition generally declining in the downstream direction. This result is consistent with the river's history of impairment of hydrology, water quality, wetland area and character, and physical form. We conclude that the reference river state based on historical conditions is unlikely to equate to the best attainable river health because certain changes have occurred in the river that may prohibit a return to the previous state of ecological health. On the basis of the results of this assessment as well as a review of the literature, we propose field data collection methodologies and indicators that can be applied in future assessments.