Macrophytes are critical primary producers in freshwater ecosystem and provide potential crop output to feed the expanding human population, they also have been used to mitigate eutrophication and upgrade the water quality. Aquatic plants adapt themselves to the more complicated, changeable and unstable conditions compared to terrestrial plants, especially the fluctuated nutrient environments. Nitrogen (N) and phosphorus (P) are the key nutrient elements for plants, and their cycles have been massively altered by anthropogenic activities in diverse ecosystems. However, there is still a lack of comprehensive understanding about the adapt mechanisms of N and P stress in aquatic plants. Therefore, we investigated the response mechanisms at the molecular, physiological, and morphological levels in the macrophyte Spirodela polyrhiza under N deficiency, P deficiency, combined N and P deficiency, and total nutrient deficiency using RNA-seq, physiological, and biochemical measurements in this study. We found that the similar response mechanisms are shared between terrestrial plants and this tiny aquatic plant, such as nutrient deficiency-induced root system architecture (RSA) changes and photosynthetic inhibition, interacting of N/P signaling networks and uptake, and the consistent changes of gene expression profiles at transcriptional level. Encouragingly, novel findings have been found in S. polyrhiza. The dramatic accumulation of starch or protein without significantly growth inhibition under nutrient deficiencies, improve the crop output of S. polyrhiza. It has a more complex P-signaling network, which is made up of miR399, PHO2, PHT1 and lncRNAs, and miR399 should be a dual-function regulator in Pi homeostasis of S. polyrhiza. The N assimilation process explained the prioritizing usage of ammonium (NH ₄ ⁺)-N in duckweed, enhancing its application to phytoremediation of NH ₄ ⁺ waste water.