Abstract. The distribution and concentration of iron in seawater and plankton were studied under different ammonium concentrations along a 22 day mesocosm experiment in order to assess possible effects of aquaculture over the phytoplankton and the biogeochemistry in fjords of Chile. Brackish and marine water were used in two different setups, each one with 1 control and 4 different NH₄⁺ concentrations. Total Chelex labile (TFe_Ch), dissolved Chelex labile (DFe_Ch) and DGT labile (Fe_DGT) iron measurements were performed in seawater, wheile the particulate iron content was determined as total (PFe) and fractionated (PFe_SF) for the plankton community. Average concentration per treatment showed higher concentrations for both TFe_Ch and DFe_Ch in the marine system compared to the brackish. TFe_Ch showed general increasing trend in time and with increasing ammonium concentration, exhibiting positive correlation to the chlorophyll and particulate organic carbon content, whereas DFe_Ch presented an inverse pattern as expected. Fe_DGT showed an average lower concentration compare to DFe_Ch with final concentrations significantly lower in treatments with artificial ammonium addition. PFe showed an increasing trend in time and with increasing ammonium in both systems. Yet, when normalized to Chlorophyll a or particulate organic carbon the trend inverted, showing that at higher ammonium loading the iron per Chlorophyll a or particulate organic carbon decreases. PFe_SF major changes occurred in the marine system in the ratio between the 20–140 μm and the 2–20 μm fractions, suggesting possible community structure shift. Overall, ammonium input indicated an effect over iron in the seawater and the particulate matter, depending on the iron form and the microbial assemblage. The further changes over the microbial composition due to ammonium addition may affect the cycling of iron, having possible negative or positive feedbacks over major biogeochemical cycles.