Environmental DNA (eDNA) has the potential to be a viable approach for detecting the existence of aquatic organisms, such as plankton. This study aimed to assess the biodiversity and composition of plankton species in the Lower Ciliwung River, Jakarta, Indonesia. During the dry season (July 2022), the study was conducted upstream to downstream of the Lower Ciliwung River. Based on read sequences, the relative abundance, biological community composition, and diversity of plankton were evaluated. In this study, a total of 1,492,975 original reads filtered to 1,265,307 reads, belonging to 22 species of eukaryotic phytoplankton and 15 species of zooplankton. The taxa identified from the eDNA samples show that order Thalassiosirales from class Mediophyceae (eukaryotic phytoplankton) and order Ploima from class Monogononta (zooplankton) were the most commonly discovered plankton. The relative abundances of eukaryotic phytoplankton and zooplankton detected in eDNA water samples did not differ significantly (p-value>0.05). The most abundant species for all sites were Stephanocyclus cryptica (phytoplankton) and Moina macrocopa (zooplankton). The eukaryotic phytoplankton and zooplankton diversity index (H’) were in the low to moderate category.