Background: Vacuoles are unique compartments in plant cells. Their multiple functions require massive fluxes of molecules across their limiting membrane, the tonoplast. Transport across the tonoplast is energized by its membrane potential and the proton gradient established by two proton pumps, the vacuolar H+-ATPase (V-ATPase), and the vacuolar H+-pyrophosphatase (V-PPase), which play important roles in the growth and development of plants. However, the mechanisms by which they affect plant growth and development, in the absence of tonoplast proton pumps, remain unclear. Results: In this study, we show that the Arabidopsis thaliana double mutant, vha-a2vha-a3, which lacks two tonoplast-localized isoforms of the membrane-integral V-ATPase subunit VHA-a, is viable, but shows a phenotype of inhibited growth and leaf chlorosis. Reduced total nitrogen absorption and increased nitrate assimilation lead to the accumulation of ammonium in the shoot, which results in the growth retardation of vha-a2vha-a3. Concurrently, the distribution and concentration of cations are abnormal in plants when VHA-a2 and VHA-a3 genes are absent, which is another major growth-limiting factor. Interestingly, the growth inhibition of the vha-a2vha-a3 double mutant was alleviated and senescence delayed, while the concentration of total nitrogen increased and that of ammonium decreased, when adding additional potassium. Conclusions: Our results show that plants can be viable without VHA-a2 and VHA-a3 but are affected by multiple factors that result in growth retardation, which can be alleviated by adding additional potassium, which provides a new insight on the relationship between vacuolar H+-ATPase and potassium.