The types and intensification of land use in the watershed affect the living organisms in aquatic ecosystems differently; this impact will also vary according to temporal and spatial scales. Understanding these interactions is crucial in the design of biomonitoring programs to detect the effect of different pollutants in freshwater ecosystems and improve watershed management and conservation strategies. Therefore, this paper qualitatively reviews biomonitoring studies in freshwater ecosystems to evaluate the impact of different land use types on multiple scales in watersheds. The paper is organized into four sections. The first section presents biomonitoring in different freshwater systems (streams, rivers, lakes, and reservoirs). In the second section, we describe the biomonitoring characteristics of the main land use types. In the third section, we explain how spatial and temporal scales affect biomonitoring. Finally, in the fourth section, we focus on biomonitoring planning and future prediction and discuss how to design biomonitoring programs and how to use models and eDNA in biomonitoring. Our review will assist in decision-making regarding biomonitoring programs in watersheds and will guide future studies on the different bioindicators for various land use types in diverse ecosystems worldwide.