Adults and children with cholestatic liver disease are at risk for type C hepatic encephalopathy (HE) and may present lifelong neurocognitive impairment. While the underlying cellular and molecular mechanisms are still incompletely understood, ammonium and bile acids (BAs) seem to play a key role in this pathology, by crossing the blood-brain-barrier and modifying neuronal homeostasis and synaptic plasticity. This experimental study aimed to investigate the effects of ammonium and BAs on dendritic spines of rat hippocampal CA1 neurons. Taking advantage of the bile duct ligated (BDL) in vivo rat model and a hippocampal organotypic rat ex vivo slice model, we analyzed dendritic spine density in both models and spine turnover ex vivo. BDL rats showed decreased dendritic spine densities after 8 weeks, paralleled with increased concentrations of blood ammonium. In organotypic hippocampal slices, exposure to ammonium, tauro-alpha-muricholic and taurocholic acid induced a decrease in dendritic spine density during the first 3 days, followed by an increase in dendritic spinogenesis during days 4-5, resulting in an increased number of dendritic spines. These observations provide new insights into the effects of ammonium and BAs on dendritic spines and consequently synaptic plasticity in chronic cholestatic liver disease.