Nanoplastics (NPs) are widely detected in aquatic ecosystems and attracting considerable attention. Although ecotoxicological impacts of NPs on aquatic biota are increasingly identified, the extent and magnitude of these detrimental effects on fish and aquatic invertebrates still lack systematic quantification and mechanistic interpretation. Here, the toxicity, influencing factors, and related mechanisms of NPs to fish and aquatic invertebrates are critically reviewed and summarized based on a total of 634 biological endpoints through a meta-analysis, where five vital response categories including growth, consumption, reproduction, survival, and behavior were emphasized to elucidate the negative impacts of NPs to fish and aquatic invertebrates from physiological to molecular levels. Our results revealed that NPs significantly decreased the survival, behavior, and reproduction of fish and/or aquatic invertebrates by 56.1%, 24.2%, and 36.0%, respectively. NPs exposure increased the oxidative stress and oxidative damage by 72.0% and 9.6%, respectively; while significantly decreased antioxidant prevention system and neurotransmission by 24.4% and 15.9%, respectively. Also, the effects of particle size, functional group, and concentration range of NPs on the physiological and biochemical reactions in the living organisms were discussed. This information is helpful to more accurately understanding the underlying toxic mechanisms of NPs to aquatic biota and guiding future studies.