Intact sediment cores were collected from the deepest basins of 12 lakes in the Rotorua District, New Zealand, to test for effects of morphological features, catchment characteristics and lake trophic state on net sedimentation rates and sediment nutrient concentrations. Multiple linear regression was used to show that 68% of the variation in net sedimentation rates across the lakes could be explained by lake trophic state and catchment area. Comparison of 2006 data with results from a survey in 1995 showed that surficial sediment (0–2 cm) total phosphorus concentrations (TP) have increased in three of the 12 lakes, at rates ranging from 27.5 to 114.4 mg P kg^–1 dry wt y^–1. Total nitrogen (TN) concentrations in surficial sediments have increased in nine of the 12 lakes at rates ranging from 51.8 to 869.2 mg N kg^–1 dry wt y^–1. Temporal changes in sediment TP and TN concentrations were not significantly linearly related (P = 0.12–0.88) to catchment area or different water column indices considered to reflect lake trophic state, including annual mean water column concentrations of TP, TN or chlorophyll a. It is concluded that between-lake variations in sediment TP and TN concentrations are influenced by a range of complex interacting factors, such as sediment redox conditions (and periodic anoxia in the hypolimnion of some lakes) as well as variations in sediment mineral composition (which influences retention and release of various sediment phosphorus and nitrogen species). Subsequently, these factors cause sediment TP and TN concentrations across the 12 lakes to respond differently to temporal changes in water column TP and TN concentrations.