Deforestation has a wide range of effects on hydrological and geochemical processes. Dissolved organic carbon (DOC) dynamics, a sensitive environmental change indicator, is expected to be affected by deforestation, with changes in atmospheric sulfur (S) deposition compounding this. However, how precisely anthropogenic disturbance (deforestation) under a declining atmospheric S input scenario affects the underlying spatiotemporal dynamics and relationships of river DOC and sulfate with hydro-climatological variables e.g., stream water temperature, runoff, pH, total dissolved iron (Fetot), and calcium (Ca2+) remains unclear. We, therefore, examined this issue within the TERENO Wüstebach catchment (Eifel, Germany), where partial deforestation had taken place in 2013. Wavelet transform coherence (WTC) analysis was applied based on a 10-year time series (2010–2020) from three sampling stations, whose (sub) catchment areas have different proportions of deforested area (W10: 31%, W14: 25%, W17: 3%). We found that water temperature and DOC, sulfate, and Fetot concentrations showed distinct seasonal patterns, with DOC averaging concentrations ranging from 2.23 (W17) to 4.56 (W10) mg L–1 and sulfate concentration ranging from 8.04 (W10) to 10.58 (W17) mg L–1. After clear-cut, DOC significantly increased by 59, 58% in the mainstream (W10, W14), but only 26% in the reference stream. WTC results indicated that DOC was negatively correlated with runoff and sulfate, but positively correlated with temperature, Ca2+, and Fetot. The negative correlation between DOC with runoff and sulfate was apparent over the whole examined 10-year period in W17 but did end in W10 and W14 after the deforestation. Sulfate (SO4) was highly correlated with stream water temperature, runoff, and Fetot in W10 and W14 and with a longer lag time than W17. Additionally, pH was stronger correlated (higher R2) with sulfate and DOC in W17 than in W10 and W14. In conclusion, WTC analysis indicates that within this low mountainous forest catchment deforestation levels over 25% (W10 and W14) affected the coupling of S and C cycling substantially more strongly than “natural” environmental changes as observed in W17.