Mucus, whereof the highly glycosylated mucins are a major component, protects the epithelial mucosal surfaces. The aim of this study was to characterize the rainbow trout (Oncorhynchus mykiss) gastrointestinal mucus barrier function, mucin production, glycosylation and response to lipopolysaccharide. Both gastric and intestinal mucus was thick and impenetrable to bacteria-sized beads ex vivo. The secreted mucus covering the gastric epithelium predominantly contained sialylated mucins. Plume-like structures emerging from the gastric pits were both sialylated and fucosylated, indicating heterogeneity in gastric mucus secreted by the surface mucus cells and gland secretory cells, whereas intestinal mucus appeared more homogenous. In vivo metabolic mucin labelling revealed regional differences in mucin production and basal to apical transport, while lipopolysaccharide stimulation increased the rate of mucin production and basal to apical transport in both stomach and intestine. Using mass spectrometry, 34 mucin O-glycans were identified, with ∼70% of the relative abundance being sialylated, ∼40% di-sialylated and 20–25% fucosylated. No effects of lipopolysaccharide treatment were apparent regarding O-glycan repertoires, relative abundance of components, size distribution or core structures. Thus, the mucus production and organization differ between epithelial sites but provide a barrier to bacteria in both stomach and intestine. Furthermore, mucin production and basal to apical transport was stimulated by lipopolysaccharide in all regions, suggesting a mechanism to combat infections.