As part of an assessment of the ecological quality of surface waters, recent European water legislation, the water framework directive (WFD), requires the setting of environmental objectives for particular chemicals. As part of this, many European countries are choosing to develop a quality classification scheme for total phosphorus (TP) concentration. The assessment of ecological quality and its component parts, such as TP, must be based on the degree of divergence of a water body from an appropriate baseline, or ‘reference condition’. For this reason, it is important to determine TP reference conditions for all lake types, or alternatively, models for predicting reference TP concentrations on a site-specific basis. With this purpose in mind, we have assembled a large dataset of European lakes considered to be in reference condition; 567 lakes in total. Data has been collated on TP concentration, mean depth, alkalinity, humic type, altitude, area, and geographical region. Reference TP concentrations have been derived from this dataset using two empirical approaches. Firstly, lake-type specific TP reference conditions were derived simply from descriptive statistics (median and percentiles) of TP concentrations by lake type. Secondly, empirical models were developed for estimating site-specific reference TP concentrations from a set of potential predictor variables. TP concentrations were found to vary with lake type and by geographical region. TP increased with colour and alkalinity, and decreased with lake depth and altitude. There was no clear relationship between TP and lake area. Altitude, mean depth and alkalinity were selected as independent explanatory variables for prediction of site-specific reference TP concentrations, with different models developed for humic and non-humic lakes. A simpler site-specific predictive model based solely on the morphoedaphic index (MEI) (a combination of a site’s alkalinity and mean depth) was also shown to be comparably effective.