Increasing trends in dissolved organic carbon concentrations in small lakes and streams have been reported across Europe and North America. Several hypotheses have been proposed, of which decreasing mineral acidity has recently been considered to be the most likely cause. The near-natural, northern Simojoki river basin (3160 km2) is located in the northern boreal zone in Finnish Lapland. Human impacts are minor with only limited forest management, low atmospheric deposition, and declining sulfate and H+ deposition over recent decades. Here we show that multiple effects (changes both in hydrological dynamics and in climate) explain increasing long-term total organic carbon (TOC) and total organic nitrogen (TON) fluxes in the river. Strong fluctuation was observed in the TOC concentration time series during the studied 43 year time period from 1962 to 2005. Statistically significant upward trends were detected for TON concentration and flow of the river during 1976–2005. The average TOC and TON flux increased by 38% and 42%, respectively, during the 1990s compared with the 1980s. The annual runoff was 27% higher during the 1990s than during the 1980s, accounting for only part of the increase in the TOC and TON outputs. Hydrological fluctuations, including longer drought/wet periods, are important. For example the drought period of 1994–1997 with low concentrations was followed by high TOC and TON concentration peaks and strong leaching fluxes during the period 1998–2000. Average soil temperatures in winter (January–April) in the 1990s were 1.6–2.1°C higher than in the 1980s. This increase may have contributed to increasing trends in organic N concentrations particularly during winter low flow, because of increased organic matter decomposition rates during the dormant season. These changes in decomposition rates might further intensify in warmer climatic conditions.