The presence of phosphorus (P) and heavy metals (HMs) in surface sediments originating from lakes Volvi, Kerkini, and Doirani (N. Greece), as well as their fractionation patterns, were investigated. No statistically significant differences in total P content were observed among the studied lakes, but notable differences were observed among sampling periods. HM contents in all lakes presented a consistent trend, i.e., Mn > Cr > Zn > Pb > Ni > Cu > Cd, while the highest concentrations were recorded in Lake Kerkini. Most of the HMs exceeded probable effect level value indicating a probable biological effect, while Ni in many cases even exceeded threshold effects level, suggesting severe toxic effects. P was dominantly bound to metal oxides, while a significant shift toward the labile fractions was observed during the spring period. The sum of potentially bioavailable HM fractions followed a downward trend of Mn > Cr > Pb > Zn > Cu > Ni > Cd for most lakes. The geoaccumulation index I values of Cr, Cu, Mn, Ni, and Zn in all lakes characterized the sediments as "unpolluted," while many sediments in lakes Volvi and Kerkini were characterized as "moderately to heavily polluted" with regard to Cd. The descending order of potential ecological risk [Formula: see text] was Cd > Pb > Cu > Ni > Cr > Zn > Mn for all the studied lakes. Ni and Cr presented the highest toxic risk index values in all lake sediments. Finally, the role of mineralogical divergences among lake sediments on the contamination degree was signified.