Metal micronutrients are essential for plant nutrition, but their toxicity threshold is low. In-depth studies on the response of light-dependent reactions of photosynthesis to metal micronutrients are needed, and the analysis of chlorophyll a fluorescence transients is a suitable technique. The liverwort Marchantia polymorpha L., a model organism also used in biomonitoring, allowed us to accurately study the effects of metal micronutrients in vivo, particularly the early responses. Gametophytes were treated with copper (Cu), iron (Fe) or zinc (Zn) for up to 120 h. Copper showed the strongest effects, negatively affecting almost the entire light phase of photosynthesis. Iron was detrimental to the flux of energy around photosystem II (PSII), while the acceptor side of PSI was unaltered. The impact of Fe was milder than that of Cu and in both cases the structures of the photosynthetic apparatus that resisted the treatments were still able to operate efficiently. The susceptibility of M. polymorpha to Zn was low: although the metal affected a large part of the electron transport chain, its effects were modest and short-lived. Our results may provide a contribution towards achieving a more comprehensive understanding of response mechanisms to metals and their evolution in plants, and may be useful for supporting the development of biomonitoring techniques.