The Lithuanian karst region covers about 1000 km3 in the northern part of the country. This is the most vulnerable area from a pollution point of view. The structure of the total dissolved solids (TDS) shows that the flow of rivers in the karst region is from hydraulically interconnected aquifers. For the last decade (1991–2000) TDS has varied considerably, from 529 to 732 mg/l. The predominant sources of nitrogen and phosphorus within the headwaters of the monitored rivers were diffuse and agricultural in nature. Downstream from the towns nitrogen and especially phosphorus showed both diffuse and point source signals. Contributions of point sources to the stream pollution by nutrients prevail.

The time series of monthly dissolved oxygen (O2) in the main karst region river – the Musa – shows the existence of multiplicative seasonality. The trend cycle (1991–1999) shows low levels of dissolved oxygen in 1991–1993, with a similar fluctuation in 1994, 1995 and 1996 (due to point pollution from the town of Siauliai) and a gradually improving situation since 1997. The general multiplicative trend of dissolved oxygen in the lower reaches of the Musa river (near the border with Latvia) is decreasing (within the accuracy limits).

The abundance and species of zoo benthos are suitable criteria (biotic index – BI) for evaluation of a river's biological water quality. Zoo benthos demonstrates tolerances that vary among species, the oxygen regime and the pollution with nitrogen. The best living conditions for invertebrates are in the riverhead of the karst region rivers – BI=5.62–6.74 (1991–1999), where pollution with nutrients is caused mostly by agricultural activity. Rare and asynchronous data of biological water quality shows up tendencies that invertebrates prefer less contaminated reaches of rivers.

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