A new special issue of New Zealand Journal of Marine and Freshwater Research, guest edited by LERNZ researchers Deniz Özkundakci and Moritz K. Lehmann, explores lake ecosystems of New Zealand and the environmental pressures threatening them. These pressures include biological invasions, nutrient runoff and climate change. This issue looks at novel methods to measure specific pressures such as the increase in cyanobacteria abundance and bloom events, and includes multi-lake studies to demonstrate the relationship between wide-reaching drivers of lake ecosystem dynamics and functions with local site-specific characteristics.