Anthropogenic activities have dramatically altered land use and land cover and have further affected the chemistry and amount of dissolved organic matter (DOM) migrating into aquatic systems, as well as the microbial community structure of lakes and reservoirs, thereby affecting the functions of lakes and reservoirs in terms of providing water resources, participating in the global carbon cycle, and supporting aquatic ecosystems. Currently, research on water quality in lakes and reservoirs primarily focuses on eutrophication. Few studies have been conducted on the effects of land cover on the microbial structure and dissolved organic matter composition of lakes and reservoirs. Additionally, there is a lack of in-depth research on the DOM composition of lakes and reservoirs due to technical constraints. In this review, we studied DOM and microbial community characteristics of seven inland lakes with three different land cover conditions (forest-dominated, cropland-dominated, and urban-dominated). And the effect of watershed land cover on the source composition of DOM in natural waters was investigated using high-resolution mass spectrometry (HRMS) characterization data of DOM using multivariate statistical analyses and the construction of co-occurrence/exclusion networks between bacterial operational taxonomic units (OTUs) and molecular formulae of DOM. The molecular composition of DOM was found to be significantly correlated with land cover and bacterial community structure, with the strongest correlation with watershed land cover. The contributions of forest, agricultural, and urban land cover to dissolved organic matter in lakes and reservoirs were organic matter in forest soils, organic matter in paddy soils, and organic matter in sewage treatment plant effluent, respectively. In addition, the sensitivity of the Acidithiobacillus to DOM composition in the water column or their key role in DOM metabolism in lakes and reservoirs was investigated. This review provides basic data support for water resource use and ecological protection of water bodies in lake and reservoirs in the context of further anthropogenic land cover in the basin in the future and is of great significance for the use of water resources in lakes and reservoirs and the protection of ecosystems in the aquatic environment in the context of the agriculturalization and urbanization of watersheds.