Climate change impacts on water systems have consequences for Indigenous communities. We documented climatic changes on water systems observed by Indigenous Shawi and resultant impacts on health and livelihoods, and explored adaptation options and challenges in partnership with two Indigenous Shawi communities in the Peruvian Amazon. Qualitative data were collected via PhotoVoice, interviews, focus group discussions, and transect walks, and analyzed using a constant comparative method and thematic analysis. Quantitative data were collected via a household survey and analyzed descriptively. Households observed seasonal weather changes over time (n = 50; 78%), which had already impacted their family and community (n = 43; 86%), such as more intense rainfall resulting in flooding (n = 29; 58%). Interviewees also described deforestation impacts on the nearby river, which were exacerbated by climate-related changes, including increased water temperatures (warmer weather, exacerbated by fewer trees for shading) and increased erosion and turbidity (increased rainfall, exacerbated by riverbank instability due to deforestation). No households reported community-level response plans for extreme weather events, and most did not expect government assistance when such events occurred. This study documents how Indigenous peoples are experiencing climatic impacts on water systems, and highlights how non-climatic drivers, such as deforestation, exacerbate climate change impacts on water systems and community livelihoods in the Peruvian Amazon.