The scientific and reasonable evaluation of heavy metals pollution in estuarine sediments is crucial for characterizing the environmental quality of the lake, however, it is still unavailable due to the lack of local geochemical baseline concentrations (GBCs) and thus applying background values of soils. In this study, the statistical method of cumulative frequency was employed to obtain the GBCs, which were applied as reference standards for the pollution assessment of heavy metals and source apportionment in estuary sediments of northwestern Taihu Lake. The results showed that the GBCs of Cd, Cu and Zn were higher than soil background values in Jiangsu Province while Ni and Pb displayed a small gap between GBCs and background values. Cd, Ni and Zn presented a degree of moderate pollution or moderate to strong pollution according to geo-accumulation index (Igeo). The pollution load index (PLI) showed that 75% of samples ranged from non-pollution to moderate pollution level while 2.94% of samples exhibited a moderate to high pollution level. The possible sources of heavy metals in the estuary sediments were quantitatively identified by positive matrix factorization (PMF), including agricultural source (23%), the combined contribution of natural sources and traffic emissions (36%) and industrial source (41%).