This study assessed the impact of pandemic-related changes in treated wastewater on surface water quality and ecological status of the Raba River within the Natura 2000 site. Particular attention to the reliability of the Kasinka Mała wastewater treatment plant operating in this protected area during the two study periods—pre-pandemic (PP) and COVID-19 (CP)—was given. For this purpose, current standard monitoring methods (ecological status of a small flysch stream, existing and potential threats to the Natura 2000 site) and extended monitoring methods (river’s utility values, technological reliability of the treatment plant operating with SBR technology, reliability rating of the river as a sewage receiver) were used. The results indicated that biodegradable carbon compounds (as dissolved and suspended forms) and ammonium nitrogen were the dominant factors determining water quality. Their presence reduced the Raba River’s utility value—determined by what is required of surface water treatment—by at least one class. During the CP, the reliability analysis showed that the river remained in a reduced class for 145 days due to elevated BOD
5 and nearly one-third of the year due to elevated TSS levels. For approximately half of the year, ammonium nitrogen concentrations exceeded the threshold of 1.8 mg·dm
−3, thereby further reducing the class of water quality. Technological reliability of the WWTP during PP for BOD
5, COD, TSS, NH
4+–N, and PO
4−3–P was 43%, 100%, 30%, 86%, and 100%, respectively. This means that permitted values of COD and PO
4−3–P were maintained. The exceedances of limits concerned BOD
5 (25 mg O
2·dm
−3 for 208 days), TSS (35 mg·dm
−3 for 256 days), and NH
4+–N (15 mg·dm
−3 for 51 days). During CP, the technological reliability of the WWTP decreased rapidly for the following pollutants to 5%, 18%, 18%, 30%, and 89%, respectively. This means that permissible concentrations of BOD
5 (25 mg O
2·dm
−3 for 347 days), COD (125 mg O
2·dm
−3 for 241 days), TSS (35 mg·dm
−3 for 299 days), NH
4+–N (15 mg·dm
−3 for 256 days), and PO
4−3–P (2 mg·dm
−3 for 40 days) were exceeded. A two-year monitoring campaign has shown that small flysch rivers receiving treated wastewater may experience prolonged changes in water quality under conditions of increased anthropopressure. Effective ecosystem protection should, therefore, include extended monitoring and stricter management of BOD
5, TSS, and NH
4+–N in SBR systems in protected areas.
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