Environmental impacts of aquaculture can be widespread and serious, and one of the problems connected to this activity is the release of waste in the form of macronutrients. One important aspect is the potential of a shift in the available nitrogen form from nitrate to ammonium. This has the potential of causing harmful algal blooms, and changing the composition of pelagic microbial communities. Because trace metals are linked to enzymatic transformations of nitrogen it can be expected that a shift in the available nitrogen form to also change the cycling of trace metals in the water column and the microbial uptake. This work presented in this thesis has been part of the large collaborative WAFOW project, and was carried out at the Huinay Scientific Field Station in the Comau Fjord (Northern Patagonian region of Chile). The experiment was designed to follow changes in different variables as a gradient of ammonium was added to different bodies of water (mesocosms). Two types of water were studied (surface and ~10 m depth), and five treatments with increasing ammonium flux were carried out for each water type. In this thesis the variations in the distribution of four different trace metals (Cd, Mo, Ni and Cu) with an increasing ammonium flux has been studied. Samples were analyzed for chelex labile and DGT labile forms of the metals, as well for metal concentration in different size fractions of particles. The enrichment by ammonium caused a bloom in biomass, and caused changes in the distribution of all four metals studied. Most of the metals showed decreasing chelex labile and DGT labile concentration with rising ammonium concentration. For cadmium there was a marked increased uptake per g carbon up to a certain point of ammonium enrichment, and a marked decreased uptake per g carbon when very high amounts of ammonium were added. This suggests that the very high ammonium enrichment scenario somehow has had an inhibiting effect on phytoplankton cadmium uptake. For molybdenum there was a decreasing uptake per g carbon with increasing ammonium flux. This is probably caused by a decreased need for molybdenum in enzymatic transformations of nitrogen when ammonium is supplied in place of nitrate.