Ecological integrity (EI), a concept referring to the structural and functional components of ecosystems, which is closely related to the integrity and stability of biotic communities, has deteriorated markedly in freshwater ecosystems across the globe. In New Zealand, many deep lakes appear to have been affected to a lesser extent by anthropogenic activities. The objective of this study was to identify and quantify a range of key in-lake indicators that could be used to report EI for deep New Zealand lakes, many of which may be expected to have high EI values. Individual indicators of EI in the lakes were related statistically to selected anthropogenic pressure indicators. Values of EI were only weakly related to the anthropogenic pressure indicators, and catchment and lake morphometric and climate characteristics were strong moderators of the relationship and suggests that monitoring of EI requires careful consideration of natural variability amongst different lake ecosystems. Physico-chemical indicators of EI tended to be more closely related to anthropogenic pressure indicators than biological EI indicators. Monitoring of physico-chemical and biological indicators in a set of reference lakes largely devoid of anthropogenic influences will help to better define elements of EI which include “nativeness”, “pristineness”, diversity and resilience.