With the rapid socioeconomic development in theLake Taihu basin, a large amount of industrial, agricultural, and domestic wastewater has been discharged into Lake Taihu, and nutrients have been enriched, especially in the northern lake regions of Lake Taihu, where algal blooms occur frequently. In the spring, summer, and fall of 2015, we conducted six field sampling campaigns at 24 sites in northern Lake Taihu’s high-incidence area of algal blooms. Absorbance coupled with three-dimensional fluorescence and parallel factor analysis (3DEEMs-PARAFAC), together with water quality parameters, were used to investigate the spatial and temporal variability of DOM and water quality in Lake Taihu under the influence of algal bloom to provide scientific support for the management and restoration of the Lake Taihu ecosystem and ensure the safety of its water supply. During the sampling period (from May 12 to October 20), the three lake regions experienced significant algal bloom and degradation. The algal blooms were closely related to the input of exogenous nutrients. During the summer, the rapid growth of algal biomass significantly consumed generated and inhibited the denitrification process of microorganisms. Parallel factor analysis identified four fluorescent DOM components: two protein-like components (tryptophan-like C1 and tyrosine-like C3) and two humic substances (microbial humic-like C2 and terrestrial humic-like C4).Terrestrial inputs from the northwest significantly affected the composition and structure of DOM in northern Lake Taihu, showing a trend of decreasing abundance and terrestrial aromaticity from west to east. In addition, the large amount of terrestrial DOM also provided an important carbon source for the growth of planktonic algae, which further influenced the composition and structure of DOM and led to the increased participation of autochthonous DOM (C2 and C3) with strong microbial activity in the lake carbon cycling process. There were differences among the three northern algal areas, and the algal bloom management in these three lakes needs to be adapted to local conditions; exogenous inputs should be reduced in the northwestern part of the lake, algal bloom monitoring and ecological restoration should be strengthened in Meiliang Bay, and ecological diversity should be preserved and restored in the northeastern part of the lake to enhance the natural purification capacity.