This in situ study used photosynthetic activity (measured as chlorophyll a fluorescence) and photosynthetic pigment concentrations to assess the effect of copper, cadmium, lead and zinc on the seagrass Zostera capricorni. Custom-made portable in situ exposure (PIE) chambers were developed so seagrasses could be dosed within the meadow. Z. capricorni was exposed to 0.1 and 1 mg l−1 of metal solutions for 10 h. During this time and for the subsequent four-day recovery period, the effective quantum yield of photosystem II (PS II) (ΔF/Fm′) was measured. While the results were variable, copper and zinc exposed samples had a depressed ΔF/Fm′ during the exposure period. Samples exposed to zinc recovered to pre-exposure levels but those exposed to copper did not. Cadmium and lead did not impact on the chlorophyll a fluorescence and the chlorophyll pigment data supported these findings. This study presents an innovative new application of chlorophyll a fluorescence stress assessment.