Duckweeds are commonly used as standard ecotoxicological test species and are excellent candidates for phytoremediation due to their adaptability to diverse aquatic conditions. This study investigated the response of two duckweed species, Lemna aequinoctialis and Spirodela polyrhiza, to mercury-contaminated environments, specifically focusing on their growth rates and photosynthetic performance under mercury stress. Duckweeds were treated with HgCl₂ at various concentrations (0, 0.1, 0.2, and 0.3 mg/L) in 10% Hoagland’s medium for seven days, after which growth parameters, pigment contents, and chlorophyll fluorescence levels were evaluated. The results showed that increasing mercury concentrations significantly affected growth and photosynthetic pigments in L. aequinoctialis and S. polyrhiza. Chlorophyll fluorescence analysis indicated that, under higher mercury concentrations, Fv/Fm and Y (II) decreased, while NPQ increased. The findings revealed that L. aequinoctialis was more susceptible to mercury toxicity than S. polyrhiza. Therefore, L. aequinoctialis may serve as a more sensitive species for mercury biomonitoring, whereas S. polyrhiza is more resistant and might, for this reason, be more useful for phytoremediation of mercury-contaminated soil.