Short-chain chlorinated paraffins (SCCPs) are organic alkanes with numerous industrial applications which are also present in some electronic devices. They are widely dispersed by wind and water, and therefore have been found in aquatic ecosystems worldwide, where they are not readily biodegradable. Organisms may thus be exposed to them in a wide range of temperatures, a factor which is known to affect a contaminant's toxicity. Thus, this work aimed to investigate the effects of SCCPs on the relative mRNA levels of multiple genes involved in vital biological functions (osmoregulation, oxidative stress, the endocrine system, immunity and antitoxic defences) of males and females of the freshwater crustacean amphipod species Gammarus pulex. They were exposed to environmentally relevant concentrations of SCCPs (10, 100, and 1000 ng/L) at two different temperatures (16°C and 20°C). Results indicate that SCCPs significantly modulated the expression of genes from all the studied functions. Furthermore, the impact of SCCPs varies depending on temperature, exposure time, and sex. The antioxidant and endocrine systems were especially impacted in females, while the other systems were affected in both sexes equally. The expression levels of more genes were altered in females than in males. This work concludes that SCCPs modify the expression levels of genes coding for antioxidant and antitoxic defences as well as endocrine functions of G. pulex at ng/L concentrations. The effects of these contaminants are under-studied in invertebrates, however these results indicate that further investigations may be warranted and needed to understand their potential effects on freshwater ecosystems.