As the recognition of the importance of biological diversity in biological conservation grows, an ongoing challenge is to develop metrics that can be used for effective conservation and management. The ecological integrity assessment has been proposed as such a metric. It is held by some to measure species composition, diversity, and habitat quality, as well as ecosystem structure, composition, and function. The methodology relies on proxy variables that include data on landscape characteristics such as patch size, abiotic factors such as hydrology, and some features of vegetation structure and composition. We suggest that the measure is flawed on four levels. First, its putative representation of general ecological form and function, and its lack of specific detail about how it actually represents those attributes, leaves the metric without the focus needed to be useful for measuring ecological features on the ground and testing associated hypotheses and predictions. Second, the proxy variables used to represent biological diversity, such as habitat (vegetation) metrics and vascular plant species diversity, are not empirically correlated with diversity of a range of taxa or of other components of the biota. Third, like other ecological indices that integrate many distinct features, the ecological integrity index is subject to the loss of information in its condensation of multi-dimensional variability into a one-dimensional index, and it may be subject to systematic bias from the conversion of raw data into categorical scores. Fourth, the sampling protocols are at risk of sampling bias, observer bias, and measurement error, any of which can confound the estimation of conservation value. In terms of biological diversity, the methodology produces an unreliable estimate of the number of vascular plant species and their relative percentages of occurrence, and an absence of any protocols for taxa other than plants. For these reasons
123Biodivers Conserv (2016) 25:1011-1035 DOI 10.1007/s10531-016-1111 we believe that ecological integrity assessment is currently of limited value as a measure of site-specific biological diversity and its change over time. A considerable amount of investigation is needed in order to have confidence in the results of an ecological integrity assessment, especially if it is to be used for regulatory purposes. We suggest further refinements and discuss alternative measures of biological diversity that provide reliable metrics for assessing change. A thoughtful choice among measures can help to identify the most appropriate assessment for conservation decisions.