Anthropogenic eutrophication and overfishing of top predators have put our lakes in danger, and coping mechanisms like The European Water Framework Directive have been put in place to mitigatetheireffects. However, the discussion on the means we employ to monitor lake ecosystems and establish their ecological status is ongoing. Importantly, it has been suggested that universal, functional indicators of healthy reference ecosystems could be identified, measured and used for comparison purposes across ecological types of lakes. An equally important issue is to develop such metrics that can be employed by lake managers, who are the end users of the scientific data when planning everyday management practices. We employed bioenergetic food web approach with Ecological Network Analysis to assess organic matter fluxes and food web structure in 13 lakes in Latvia – including 3 pristine bog lakes - and combined the acquired functional descriptors with simple and well-known ecological descriptors. We conclude that information on the functioning of pristine lakes provides a potentially valuable tool for setting functional reference conditions for lake management. We also found that the ecological parameters - the percentage of piscivorous fish and the abundance of cyanobacteria - correlate well with the functional food web descriptors. Thus, they could be valuable tools to both managers and scientists when evaluating lake ecological status across the boundaries of ecological types.