The contemporaneous effect of natural and anthropogenic factors involved in a watershed contribution to the seasonal and spatial variation of diatom community composition is widely discussed in the scientific literature. Yet, there is a paucity of scientific evidence indicating the effect of these factors on diatoms in tropical African regions characterized by distinct dry and wet seasons and season associated human activities like rainfed agriculture are commonly practiced. We applied multivariate techniques to determine the spatio-Temporal drivers of diatom assemblage and diatom species richness in human influenced rivers and streams in Ethiopia. We simultaneously collected water and diatom samples from 24 sampling points during the wet (July) and dry (February) seasons. Both water and diatom samples were processed following standard procedures. We identified 169 species belonging to 45 genera in the studied lotic systems. We found that both season and land use factors were important in defining diatom composition (PERMANOVA, p0.05) and species richness (ANOVA, p0.05) patterns. Diatom community composition was driven by conductivity, dissolved oxygen, pH, and turbidity parameters (Monte Carlo permutation test, p0.05). Besides, diatom species richness was driven by dissolved oxygen, soluble reactive phosphorus, and turbidity (GLMM, p0.05). The study highlighted physicochemical parameters influenced by seasonal variation and human activity determined the composition of diatoms. This implies that the unique feature of heavy rain during the rainy season in the region followed by extensive flooding aggravated by the steep slope from the highlands to the lowlands plays a major role in shaping the diatom autecology in the region. Therefore, in applying biomonitoring in such regions considering the effect of runoff and dilution is imperative.