ABSTRACT: Our understanding of the ecological consequences of human activities may change based on our choice of taxonomic classifications used to observe ecological patterns. We tested the effects of water pollution (nutrient enrichment) and over-harvesting (loss of grazers) on several measures of algal abundance and diversity. These measures included the percentage cover and biomass of individual species and morphological groups, as well as indices that aggregate the response of species, i.e. species diversity (Shannon index) and the less commonly used Abundance-Biomass Comparison (ABC) curves and phylogenetic diversity. Together, all observed responses suggested that nutrients had the largest effect, whether positive (e.g. biomass of sediment-trapping algae), negative (e.g. phylogenetic diversity), or exacerbated by loss of grazers. The interaction between nutrients and grazers was only detected by 2 indices that relied on phylogenetic classifications (ABC curves and phylogenetic diversity). The more traditional aggregate index (Shannon index) did not detect the effect of either nutrients or grazers. Non-indices (i.e. biomass of morphological groups) were sensitive only to the experimental influence of nutrients, whereas observations of individual species alone could not detect the effects of any treatments. These differences highlight the importance of classification (e.g. morphology versus species) and indices (e.g. Shannon index versus ABC curves and phylogenetic diversity) in their potential to predetermine our perception of ecological change and predictions of future environments.