Phytoplankton species composition has long been recognized to be structured by environmental filtering, but our knowledge of patterns of spatial dissimilarity congruence between the phytoplankton community and environmental divers is rather limited. Specifically, a study on whether there are specific temporal properties that could be more related to spatial dissimilarity remains to be seen. We examined the extent to how spatial dissimilarity changed with seasonal succession by measuring beta-diversity in phytoplankton communities in Lake Erhai (from January 2012 to December 2014 at 15 sampling sites) as a function of different period conditions (high-density period and low-density period). We found that congruences of spatial dissimilarity in algal communities over time were neither stable in time nor showed a seasonal pattern. The spatial dissimilarity congruence between the phytoplankton community and dissolved inorganic phosphorus (DIP) concentration followed exponential decay patterns, and this congruence was led by algal cell density. This result implies that species and functions of phytoplankton are specialized, and DIP concentration drastically increases in high-density periods than in low-density periods. This means that DIP enrichment is related to the loss of algal diversity and functions and the increase of algal biomass in eutrophic lakes.