Trace metal micronutrients are known to play an important role in the optimal functioning of aquatic microorganisms involved in the sequestration of atmospheric carbon dioxide. Understanding the biogeochemical cycling of trace metal micronutrients in the global ocean has been a focus of intense research over several decades. Conversely, investigations into the cycling of trace metals in lakes have been relatively rare. This study investigated the biogeochemical cycling of five biologically important trace metals, namely manganese, cobalt, nickel, copper and zinc in three New Zealand lakes of different trophic state. The surface water in the three lakes was sampled monthly over a year, during which depth profile samples were collected twice. The samples were analysed to examine how trace metal speciation and phytoplankton productivity interact in the three lakes over time. The cycling of the metals was driven by the different physicochemical and biogeochemical factors distinctive for each lake, including water column oxygen concentrations and the extent to which each metal was bound to particulates. Intriguingly, increased biological uptake or limitation of growth during times of high phytoplankton growth was not observed for any of the investigated trace metals. This is of interest, especially as many of the trace metals investigated were present in sub-nanomolar bioavailable concentrations. The results from this study emphasise the important role biogeochemical cycling plays in regulating the distributions and bioavailability of trace metals in lakes.