The microorganism community that grows under duckweed shelter can play an important role on treatment processes. Therefore, the present study aimed to assess the zooplankton dynamic and microbial community in duckweed ponds (DPs) applied for domestic wastewater treatment under open field conditions. A pilot system comprised of two DPs in series (DP1 and DP2), with 10 m2 each, received domestic wastewater through a flow rate of 200 L·day−1. Thus, the system was monitored during 314 days through samples collected and analysed weekly. Also, the zooplankton organisms were identified and quantified. DNA sequencing was performed in order to identify the bacterial populations. The findings showed a high efficiency of nutrient removal with 93% and 91% of total phosphorus and total nitrogen, respectively. A high density of microcrustaceans was observed in DP1 reaching 4,700 org.100 mL−1 and rotifers (over than 32,000 org.100 mL−1) in DP2, that could be related to the low suspended solids concentration (<30 mg·L−1) and turbidity (<10 NTU). The bacterial community showed a strong heterogeneity between samples collected along the seasons. Through these findings, it is possible to realise that the understanding of ecology could help to enhance the operation and designs of DPs.