Restoration and management of lake ecosystems require an understanding of natural variability in primary productivity and the factors that drive change. To understand long-term changes in, and relationships amongst phosphorus species and phytoplankton groups, a sediment core was retrieved from Lake Okataina in the central North Island of New Zealand. The core was dated to include a period of approximately 700 years, from pre-human settlement to its current state, close to natural reference conditions. Pigments representing different planktonic groups were measured vertically through the core at 1 cm intervals, as well as phosphorus fractions associated with apatite and CaCO3, Fe and Mn (oxy) hydroxides, Al (oxy) hydroxides and labile phosphorus. Highly significant correlations were established amongst the algal groups and the phosphorus species. Diatoms were strongly correlated with phosphorus fractions associated with permanent burial, while cyanobacteria and green algae were correlated with potentially bioavailable phosphorus. Green algae, cyanobacteria and cryptophytes co-dominated when diatom populations were reduced, and vice versa. Using multiple linear regression, phosphorus fractions could be used to hindcast historical variations in the composition of algal communities (as inferred from pigments), with the exception of alloxanthin (representative of cryptophytes). Our approach provides a technique for a relatively rapid assessment of long-term changes in the major phytoplankton groups in lakes and may be used to infer natural variability in the reference state as well as partitioning the extent of alteration of phytoplankton community composition between human and natural disturbances.