The paper deals with nutrient runoff monitoring results and calculated nutrient budgets on catchment level in small agricultural watersheds in Estonia. A special programme for monitoring of nutrient losses was initiated and a network of monitoring stations, equipped with data-loggers and suitable devices for continuous flow measurement and flow-proportional automatic water sampling were established in Estonia in the mid-1990s. The research methodology is harmonized with the Nordic countries as well as with the other Baltic countries. The results indicate that nutrients losses are relatively low (generally below 11 kg N/ha and 0.9 kg P/ha). It can be partly explained by drastic changes in the Estonian agricultural practice in the 1990s but also by differences in runoff regime.

Nutrient balances were calculated for two catchments, based on the data collected from the farms, some special studies and water quality monitoring results in two watersheds in 1995 (1999) - 2001. The nutrient balances for the catchments turned positive after being negative both for nitrogen and phosphorus in the mid-1990s.

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