Nitrogen lost from agriculture has altered the geochemistry of the biosphere, with pronounced impacts on aquatic ecosystems. We aim to elucidate the patterns and driving factors behind the N fluxes in lowland stream ecosystems differing about land-use and climatic-hydrological conditions. The climate-hydrology areas represented humid cold temperate/stable discharge conditions, and humid subtropical climate/flashy conditions. Three complementary monitoring sampling characteristics were selected, including a total of 43 streams under contrasting farming intensities. Farming intensity determined total dissolved N (TDN), nitrate concentrations, and total N concentration and loss to streams, despite differences in soil and climatic-hydrological conditions between and within regions. However, ammonium (NH4+) and dissolved organic N concentrations did not show significant responses to the farming intensity or climatic/hydrological conditions. A high dissolved inorganic N to TDN ratio was associated with the temperate climate and high base flow conditions, but not with farming intensity. In the absence of a significant increase in farming N use efficiency (or the introduction of other palliative measures), the expected farming intensification would result in a stronger increase in NO3−, TDN, and TN concentrations as well as in rising flow-weighted concentrations and loss in temperate and subtropical streams, which will further exacerbate eutrophication.