Insufficient wastewater remediation in small communities and nonpoint source pollution are the key factors in determining the water quality of small streams in an agricultural landscape. Despite the current extensive construction of municipal wastewater treatment facilities in small communities, the level of organic substances and nutrients in the recipient catchments has not decreased in many areas. This paper analyzes the changes in the water quality of the small streams after the deployment of wastewater treatment plants that were designed to address sources of pollution from small municipalities. The analysis is based on the results from a water quality monitoring network in the small watersheds in the Czech Republic. Five rural catchments with one dominant municipal pollution source, where a wastewater treatment plant was deployed during the monitoring period, were selected according to a predefined set of criteria, from a series of 317 profiles. Basic water quality indicators were selected for the assessment: O₂, BOD-5, COD, TOC, conductivity, NH₄-N, NO₂-N, NO₃-N, PT, and PO₄-P. Results of the analysis showed that the simple deployment of the water treatment facilities at these streams often did not lead to a reduction of contamination in the streams. The expected post-deployment changes, namely, a significant and permanent reduction of stream contamination, occurred only in one catchment, whereas in the remainder of the catchments, only marginal changes or even increased concentrations of the contaminants were detected. As the critical factors that determined the efficiency of wastewater treatment were studied, the need for the consideration of the local conditions during the design of the facility, particularly regarding the size of the catchments, initial level of contamination, proper system of operation, and process optimization of the treatment facility, emerged as the important factor.