Selenium nanoparticles (SeNPs) have been applied in the biomedical and biocidal domain which may have potential environmental risks for aquatic systems. However, the knowledge of its toxicity and the role of functionalization on aquatic invertebrates are scarce. Thus, the present study aimed to analyze the embryotoxicity of two types of SeNPs coated with Sodium carboxymethyl cellulose (CMC-SeNPs) and Chitosan (CS-SeNPs) to the freshwater snail Lymnaea stagnalis in lake water, focusing on embryonic development. The influence of surface coatings and ions release, on the embryonic development of SeNPs to freshwater snail L. stagnalis was investigated. For this end, the snails were exposed to different concentrations of SeNPs and Se ions (0.05–1 mg L􀀀 1) during 7 days and multiple endpoints were analyzed, including developmental stage frequency, morphological alterations, embryos mortality and hatching success. The results showed that both Se forms promoted the developmental delay, mortality, morphological changes, and hatching inhibition in snail embryos in a concentration-dependent manner. CMC-SeNPs are 2.6 times more embryotoxic compared to CS-SeNPs indicating the importance of surface coating on the embryotoxicity. Moreover, the results revealed that although both forms of Se inhibited the embryo development and reduced the hatching of L. stagnalis, the mode of action on the embryogenesis was different. SeNPs had a higher toxicity to snails’ embryos compared to their dissolved counterparts. Despite significant dissolution, by comparing the SeNPs with their dissolved fraction, the results suggest SeNPs inhibition effect on the snail development could be caused by both SeNPs and Se4+, and SeNPs might be the major development retardation driver rather than Se ions. The present study evidenced by the first time the toxicity effects of SeNPs on the snail embryogenesis, and highlighted how SeNPs intrinsic properties influence their transformation and toxicity in environmental relevant scenarios.