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Artificial subsurface drainage systems are a common water management practice to remove excess water from agricultural land in the Baltic and Nordic countries. Unfortunately, these systems also serve as nutrient transport pathways from agricultural fields to downstream waterbodies. The objective of this study was to determine the status of subsurface drainage water in the context of implementation of the European Union (EU) Water Framework Directive (WFD) and EU Nitrate Directive (ND), to investigate the impact of hydrology and mineral fertilizer application on nutrient losses through subsurface drainage systems and to evaluate the possible effects of climate change on drainage and nutrient loss. This research was conducted from 1995 through 2013 at the agricultural run-off–monitoring sites in Berze and Mellupite. Continuous-flow measurement data and composite water samples were collected on a monthly basis for assessment of total nitrogen (TN), nitrate–nitrogen (NO3–N) and total phosphorus (TP) in drainage water. Results from the study indicated that the mean annual NO3–N concentration was slightly below the threshold level defined by ND, while TN concentrations exceeded the threshold level for good chemical status of water according to WFD. Differences in TN losses were mainly driven by the hydrologic behaviour at the study sites rather than by mineral fertilizer application rates, whereas TP losses under similar application rates were affected by open inlets for surface water accumulation. The comparison of meteorological data for the research period (1995–2013) with the long-term mean (1950–1994) showed a pronounced evidence of climate change. The mean annual precipitation amount has increased at both Berze and Mellupite monitoring sites by 36 mm and 42 mm, respectively, compared to the long-term mean for 1950–1994. Meanwhile, the mean annual temperature during the research period was 7.3°C for Berze and 6.4°C for Mellupite, which is 1.4°C and 0.6°C warmer than long-term mean. [ABSTRACT FROM AUTHOR]