Concerns about water pollution from commercial agriculture, demographic changes, urbanisation, industry, and anthropogenic activities in the Ngwerere River peri-urban watershed (NPW) were the drivers of this study. This study focused on the spatial vulnerability of surface water to chemical pollution. The aim was to implement a rapid integrated ecosystem assessment system to analyse the predisposition of surface water to chemical pollution. The specific objectives were to evaluate water quality (WQ) parameters as indicators of chemical pollution in the Ngwerere River, determine the spatial vulnerability of water to chemical pollution, and establish linkages between chemical pollution and sources within the NPW. In this study, the ecosystems approach, was followed to assess pH, salinity, total dissolved solids (TDS), chemical oxygen demand (COD), Na+, and total suspended solids (TSS) to determine WQ for the functional integrity of some ecosystem services. The results show that pH ranged from 7–8 and COD from 4–36 mg L-1 O2. The results for other parameters were as follows: 60–163 mg L-1, 258–567 mg L-1, 22–60 mg L-1, and 2–710 mg L-1 for salinity, TDS, Na+, and TSS, respectively. The means were 7.62 ± 0.05 mg L-1, 118.50 ± 4.07 mg L-1, 437.91 ± 14.35 mg L-1, 17.45 ± 2.04 mg L-1 O2, 45.46 ± 1.53 mg L-1, and 192.79 ± 46.90 mg L-1 for pH, salinity, TDS, COD, Na+, and TSS, respectively. With the exception of COD and Na+, which exceeded the relevant environmental standards, all measured parameters were within acceptable ranges, indicating the functional integrity of the ecosystem. Furthermore, the trends in concentration for all WQ parameters were indicative of chemical pollution. Three watershed positions, upstream catchment (USC), midstream catchment (MSC), and downstream catchment (DSC), were assessed for vulnerability to chemical pollution. USC and MSC were more vulnerable based on all parameters, excluding TSS, which had higher concentrations at DSC. Linkages were established between chemical pollution in the river and pollution sources. With the exception of TSS, all parameter concentrations were high in USC and MSC due to their proximity to point source and non-point source pollution. In contrast, high concentrations of TSS were observed in DSC due to the accumulation of loading. Further work should be conducted to establish the ecosystem services present in NPW. Thus, assessments will need be refined and focused on specific environmental concerns for NPW.  Keywords: chemical pollution, ecosystems, freshwater, water quality, Ngwerere River peri-urban watershed