The conference ‘Ecology of Fish in Lakes and Reservoirs’ (ECOFIL 2014) was held in September 2014 in České Budĕjovice, Czech Republic. More than 110 lectures and posters presented during the meeting documented rapid methodological developments in freshwater fisheries science and recent advances of studies of biotic integrity and quality of fish stocks required by the EU Water framework Directive and the US and Canadian Fisheries Agencies. Most contributions focused on the main conference themes of the role of fish in trophic webs, spatiotemporal patterns, effects of environmental and anthropogenic stressors, fisheries management and ecological status.