Two hydrolysis techniques were tested to optimize hydrolysis conditions for natural lake polysaccharides (PS). Modified sulphuric acid hydrolysis was found to be more efficient than 0.1 M HCl hydrolysis as assessed by a spectrophotometric method commonly known as TPTZ assay (2,4,6-tripyridyl-s-triazine). Capillary electrophoresis coupled with laser induced fluorescence (CE–LIF) was standardized to determine hydrolyzed saccharides in water. Two types of capillaries were tested for the CE technique. Fused silica capillary was found good for quantitative determination of different saccharides (r ² = 0.998, P<0.001). Excellent resolution of monosaccharides was achieved using a gel capillary (CGE), but correlation coefficients (r ²<0.87, P<0.05) were not as strong as in the case of silica capillary. CE–LIF and TPTZ assay were applied to quantify the vertical polysaccharide profile of the Lake Geneva (0–309 m). Maximum concentration of PS (1.02 ± 0.03 mg L⁻¹) was observed at surface. The concentration gradually decreased, with a minimum concentration of PS at 290 m (0.27 ± 0.04 mg L⁻¹). A fairly good correlation (r ² = 0.83, N = 9, P<0.001) between the total organic carbon (TOC) and APTS saccharide adduct measured by fused silica capillary was observed. The vertical profile of the lake as determined by CGE indicated glucose and fructose as dominant sugars with a minor contribution of xylose. The present study indicates the potential of CGE for qualitative as well as quantitative analysis of hydrolyzed saccharides in water samples.