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Trophic state of lakes has been related to catchment land use, but direct links between phytoplankton taxa and land use are limited. Phytoplankton composition, represented by relative cell abundance of phyla, was measured over a period of 4 years in 11 lakes in the Rotorua region, New Zealand. The lakes differed in morphometry, trophic state and land use (as percentage catchment area). We tested whether relative proportion of land uses, indirectly representing relative nutrient loading, was the overarching driver of phytoplankton composition. Trophic state was correlated negatively with native forest and positively with pasture and urban area. Cyanoprokaryota were correlated negatively with native forest and positively with pasture and trophic state, Chlorophyta were correlated positively with native forest and urban land use and negatively with pasture and trophic state, and Bacillariophyta were positively correlated with dissolved reactive silica to dissolved inorganic nitrogen (Si:DIN) and Si to dissolved reactive phosphorus (Si:DRP) ratios. Lakes with higher nutrient loads had higher trophic state and Cyanoprokaryota dominance. Chlorophyta were negatively correlated with Cyanoprokaryota and Bacillariophyta, suggesting competition amongst these groups. Our results apply to lakes potentially subject to changes in catchment land use, which may have implications for trophic state, phytoplankton composition and Cyanoprokaryota blooms.