Nutrient enrichment is one of the most pervasive impacts on aquatic ecosystems globally. While the range of impacts are well documented, approaches used to establish nutrient criteria that safeguard aquatic ecosystem health are varied and challenging. In many instances, criteria are derived from correlations between in-situ nutrient concentrations and biological indicators. However, summarising entire assemblages as a single biological indicator can result in a substantial loss of information and potentially weak relationships. In this study, we compared the derivation of nutrient criteria for rivers and streams using biological indices with those from individual taxa. Random forests were used to model the probability of passing targets for two biological indices, and the probability of occurrence of individual macroinvertebrates, with increasing nutrient enrichment across all New Zealand’s riverine monitoring network. We observed substantially greater performance in modelling the probability of occurrence for individual taxa than probability of passing targets of the two biological indicators. Nutrient concentrations were almost always the most influential factor predicting the distributions of individual species. To protect 80% of taxa within a river reach from a large change in probability of occurrence because of nutrient enrichment, we estimated that DIN (Dissolved Inorganic Nitrogen) concentrations would need to be below 0.57-1.32 mg/L, and DRP (Dissolved Reactive Phosphorus) concentrations below 0.019-0.033 mg/L. In general, high order, low slope, rivers and streams required more stringent nutrient criteria than steep, low order streams. We observed considerably stronger relationships between nutrients and individual taxa, which potentially allow for more accurate and robust nutrient criteria to be derived. We consider that the derivation of nutrient criteria for waterways should not rely solely on relationships with biological indicators, as is commonly practiced, but also involve examination of relationships with individual taxa as established to protect a desired proportion of taxa.