Freshwater plants play a pivotal role in the health and functioning of freshwater ecosystems, and they also offer a variety of benefits to humans. Despite their importance, there is a significant gap in our understanding of the macroecology of freshwater plants in tropical regions, where biodiversity is typically high, and ecosystems face substantial pressures from human activities. To bridge this knowledge gap, we conducted extensive field surveys and applied statistical methods to understand the patterns of distribution, density, and diversity of freshwater plants and their relationship with abiotic components in four freshwater lakes in Kenya. We aimed to answer four key questions: (1) How many freshwater plant species occur in these lakes? (2) What proportion of these freshwater plant species are native and alien to Kenya? (3) What proportion of these species have a history of being invasive somewhere in the world, including in Kenya? (4) Which water and sediment characteristics are significantly associated with the presence, density, and diversity of freshwater plants in the lakes? We inventoried a total of 163 freshwater plant species, of which 114 were native to Kenya and 49 were alien. Online database searches revealed that 114 species had a history of invasion globally, with 22 species already invasive in Kenya. Our statistical analysis showed that the presence and density of plant species were positively correlated with pH and turbidity, but negatively correlated with soluble reactive phosphorus in both water and sediments, ammonia-nitrogen in sediments, and nitrate-nitrogen in water. Shannon-Wiener diversity of the plant species was positively correlated with ammonia-nitrogen in water and nitrate-nitrogen in sediments but negatively correlated with longitude and electrical conductivity of the water. Pielou’s evenness within the communities showed positive correlations with soluble reactive phosphorus in both water and sediments, ammonia-nitrogen in sediments, and nitrate-nitrogen in water but was negatively correlated with water turbidity and pH. The number of species with a history of invasion was positively correlated with longitude and electrical conductivity but negatively correlated with ammonia-nitrogen and nitrate-nitrogen in water. This extensive inventory not only enriches our understanding of the biodiversity within these freshwater plant communities but also highlights the potential risks posed by species with a history of being invasive. The findings regarding environmental variables linked to the presence, density, diversity, and invasive potential of these species underscore the complexity of freshwater ecosystems and the array of factors influencing the composition of freshwater plant communities.