Polyaluminum chloride (PAC) coagulation, short wavelength ultraviolet (UV-C at 254 nm) treatment and UV-C/PAC treatment of algae-laden water from Meiliang Gulf (Lake Taihu) were conducted. The intrinsic characteristics and correlations of chromophoric dissolved organic matter (CDOM), algae biomass and other contaminants were investigated. Parallel factor analysis determined four CDOM components, and principal component analysis (PCA) identified three integrated principal factors. PCA Factor 1 had correlations with dissolved organic carbon (DOC) (r = 0.798), UV254 (0.645), humic-like CDOM component C3 (0.892) and C4 (0.876), and Factor 2 correlated with in vivo chlorophyll-a (0.768), microcystin-LR (0.713), protein-like C1 (0.782) and C2 (0.759). Factor 3 had correlations with NH3-N (0.851) and total phosphorus (T-P) (0.716). The variation in PCA factor scores revealed that single PAC coagulation preferentially removed algal cells (Factor 2) but had little effect on NH3-N and T-P (Factor 3). Single UV-C treatment induced degradation of protein-like CDOM and decrease of algal biomass (Factor 2), followed by humic-like CDOM increase from ruptured cells (Factors 1 and 3). Compared with single PAC coagulation (20 mg L−1), the combined UV-C/PAC treatment (700 mJ cm−2 + 20 mg L−1) enhanced the removal of PCA Factors 1, 2 and 3 (15%, 32% and 10%).