Large-scale water transfer projects can be an important way of mitigating water scarcity and have been adopted worldwide. Nevertheless, investments in massive infrastructure, negative environmental impacts and restrictive legislation have required water managers to adopt new approaches, such as small-scale inter-basin water transfer (SSIWT), especially in industrial and urbanized regions. However, there is a lack of research concerning environmental impact assessments of SSIWT to support decisionmaking, notably in developing countries (such as Brazil). The main goal of this research was to assess the environmental impacts of water transfer on the quality of surface water in the Jundiaí-Mirim river basin, southeast Brazil. Water samples were collected along the Jundiaí-Mirim River in September 2013 (in the absence of SSIWT) and in September 2014 (during SSIWT) for determining the following parameters: pH, temperature, turbidity, electrical conductivity (EC), dissolved oxygen (DO), total organic carbon (TOC), dissolved organic carbon (DOC), total phosphorus (TP), total nitrogen (TN), chloride (Cl −), chlorophyll-a (Chl-a) and dissolved and total metals (Al, Cd, Cu, Fe, Mg and Mn). Descriptive statistics and the paired Student's t-test (p < 0.05) were used to test the hypothesis that there was an effect of SSIWT on water quality. The results showed impacts due to the transfer of ions from the Atibaia River to the Jundiaí-Mirim River, as well as the degradation of riverbanks, which significantly (p < 0.05) influenced DO, TOC, DOC, TN, Cl − , Al, Fe and Mg concentrations. A positive impact on the trophic state was observed due to the increased flow caused by the water transfer, which acted to flush the river and reservoir. The findings provide important information on the environmental performance of small-scale hydraulic operations, which should assist decision-makers in establishing strategies to reduce negative environmental impacts.