The aim of this study was to determine the change of water quality in the Trzemna River after modernisation of the wastewater treatment plant (WWTP) in Gołuchów and wastewater effluent diversion (WED) to the Prosna River in 2008. Data was acquired from the State Environmental Monitoring database for the period before and after changing the location of discharge from the treatment plant. The before-after (BA) and before-after-control-impact (BACI) analyses were used to determine the effectiveness of applied solutions. The BA study covered 12 physicochemical parameters and showed improvement of water quality in terms of phosphorous compounds, EC, ammonium nitrogen, TKN, TN, and BOD5. Lack of statistically significant differences for nitrates, pH, and TOC were noted. The BACI analysis was only applicable for six physicochemical parameters, and statistically significant differences were shown for TN, TKN, ammonium nitrogen, and TP. There were no differences in the case of nitrates and DO. After wastewater effluent diversion, a high concentration of nitrates in Trzemna water was still observed, with a statistically confirmed increasing trend. This is an effect of the negative impact of agricultural diffuse pollution. Modernisation of a WWTP and wastewater effluent diversion positively affected the quality of Trzemna water. The BA and BACI analyses in relation to statistical tests applied in hydrology can be successfully used to evaluate the impact of changes in the environment on water quality. In the case of BA design it was possible to analyse 12 parameters, whereas in BACI analysis it was only half of them. However, this method is recognised as more reliable and eliminates the impact of natural temporary variations.