The waste slurry produced by the dredging of urban rivers needs to be dewatered before being reused sustainably. As a large amount of plant debris accumulates in sediment, humus-like substances become one of main components in waste slurry. In light of the lack of research on the effect of fulvic acid (FA) in waste slurry on flocculation and separation, this paper carried out experimental research, including the effect of FA content on flocculation and filtration, as well as flocculation and filtration experiments of eight different sources of waste slurry. The results show that if only the FA content in the slurry is changed, the effect of FA on flocculation and separation is significant when the FA content is 0~3%, but it is not obvious when the FA content exceeds 3%. The flocculation and filtration results of eight different sources of river-dredged waste slurry are obviously different; the D10 increment can differ by nearly 10 times, and the specific resistance to filtration (SRF) differs by 2 orders of magnitude. However, FA is not a sensitive factor affecting the flocculation results. FA mainly affects the results by affecting the zeta potential of the slurry. Therefore, in the dewatering design of waste slurry, only the zeta potential needs to be considered.