Water clarity, denoted by the Secchi disk depth (SDD), is one of the most important indicators for monitoring water quality. In the Songhua River basin (SHRB), few studies have used Landsat to monitor long-term (3-4 decades) changes in lake SDD and explore the impact of natural and human factors on SDD interannual variation at the watershed scale. Lakes in the SHRB are of great significance to local populations. Understanding the spatiotemporal dynamics of SDD could help policymakers manage, protect, and predict lake water quality. We utilized the Landsat red/blue band ratio in the Google Earth Engine to estimate the SDD of 77 lakes and generated annual mean SDD maps from 1990 to 2018. The results of the SDD interannual changes showed that the water quality in the SHRB has improved since 2005. Specifically, the SDD in the SHRB displayed a significant increasing trend (p<0.05) from 0.29 m in 2005 to 0.37 m in 2018. Moreover, the number of lakes displaying a significant increasing trend for SDD increased from 18 between 1990-2005 to 31 between 2005-2018. We also found that use of chemical fertilizer significantly impacted lakes, followed by wastewater discharge and normalized difference vegetation index. Improvements in the quantity and ability of wastewater discharge treatment and increased vegetation cover have alleviated water pollution; however, the non-point pollution of agriculture still poses a threat to some lakes in the SHRB. Therefore, more efforts should be made to further improve the aquatic ecological environment of SHRBs.