The potential of aquatic plants to accumulate Cs may be of notable importance in the environmental monitoring of radioactive wastes. This study aimed to evaluate the accumulation of Cs-133 by freshwater macrophytes Bacopa amplexicaulis, Elodea densa, Ceratophyllum submersum, and Limnobium laevigantum after a 10-day incubation period with CsCl (1–1000 μM). The partitioning of Cs and other elements, including 21 metals, such as P, B, and As, was analyzed using inductively coupled plasma mass spectrometry combined with principal component analysis (PCA). The enzymatic activity of plant crude extracts and aquatic microorganisms was characterized. The transfer factor (TF) reached the highest values of 0.13 and 0.10 for C. submersum and L. laevigantum, respectively, at 1000 μM Cs. The TFs in the other sets were below 0.1. In the presence of Cs-133, there was a significant increase in dehydrogenase activity (p < 0.05) and a decrease in the activity of the Folin–Ciocalteu assay. A three-fold decrease in culturable microorganisms was found in plants with 1000 μM Cs. PCA analysis revealed the species-specific elemental distribution in plant biomass and the aquatic phase. A negative correlation between Na, Ca (2.0–2.5, PC1) and Mg, K, and P (−2, PC1) was found. Certain enzyme groups can serve as bioindicators of Cs pollution in aquatic ecosystems.