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The most populous city of the world’s largest watershed (Manaus, Amazon Basin, Brazil) is experiencing an extensive urban expansion since the early 1970s, with an attendant cost in environmental degradation. The upland area of the Manaus municipality is characterized by several streams. In this work, we aim to gradually measure the anthropogenic effect on water quality: we monitored three streams flowing over three zones: a preserved (where the streams take source), a peri-urban (where rural and leisure activities occur), and an urban area. From June 2013 to May 2015, we characterized the water quality of these streams. Statistical analyses reveal peri-urban activity does not significantly impact the water quality. Indeed, when the disturbance remains space-, time- and intensity-limited, the streams have the capacity to assimilate the anthropogenic pollution. However, looking at a seasonal finer scale, peri-urban activity slightly affects the natural pattern of water quality, but these changes remain moderated when compared to the original pattern of water quality. Over urban area, the water quality presents significant higher alkalinity, mineralization, turbidity, suspended material, biochemical and chemical oxygen demands, and lower acidity and dissolved oxygen. These alterations originate with sewage deficiency, presence of landfill sites, enhanced leaching of upturned soil and domestic waste. The natural seasonal patterns of water quality are totally disturbed (inversion, intensification) in the urban area. During the wet season, enhanced rainfall in conjunction with human activity generates local seasonal processes of dilution (e.g. negative anomalies for most of the dissolved elements) and concentration (positive Mg and Fe anomalies). The latter can be linked with enhanced leaching during the rainy period (positive Mg and Fe anomalies) and nitrification activity in the urban area (positive NO3 and negative NH4 anomalies).