The impact of sapropel of Lake Tarosiškis on photosynthesis parameters (content of pigments and chlorophyll a fluorescence) of beans (Vicia faba L.) was investigated in this study. Plants were sown in 1 L volume pots by 5 seeds with light loamy soil and grown in growth chambers. Considering sapropel composition, 2.2, 3.1 and 4 t/ha dry sapropel concentrations were chosen for investigation. Sapropel-affected plants were compared with plants grown in unfertilised soils and soils fertilised with a synthetic fertiliser. On day 14 of the experiment, when the plants reached 2-leaves growth stage (BBCH 12), chlorophyll a fluorescence parameters of the investigated plants were measured. Then the plants were grown for another 4 weeks, and at the stem elongation stage (BBCH 31), chlorophyll a fluorescence parameters were measured repeatedly and the content of chlorophylls and carotenoids was investigated. The photosystem II efficiency of beans insignificantly increased (p > 0.05) by increasing sapropel concentration in the soil. Photosynthesis performance index increased (r = 0.91; p < 0.05) with increasing sapropel concentration up to 3.1 t/ha at BBCH growth stage 12. The same tendency was observed for the electron transport rate of beans (r = 0.9; p < 0.05) at this growth stage, but at a later stage (BBCH 31) it slightly lowered (r = -0.02; p > 0.05). At BBCH stage 12, the highest non-photochemical quenching (NPQ) value was measured in control beans, while at BBCH stage 31, the opposite trend was noticed (r = 0.86; p < 0.05). At BBCH growth stage 31, an increase in sapropel concentration made the bean chlorophyll content to decrease; however, this decrease was insignificant (r = -0.18, p > 0.05). The changes in the carotenoid content were similar to chlorophyll a+b.