Deforestation can lead to an increase in the availability of nutrients in the soil and, in turn, have an impact on the quality of water in receiving water bodies. This study assesses the impact of deforestation by evaluating the in-stream concentrations of dissolved organic carbon (DOC) and nitrate, their internal relationship, and those with stream discharge in the Wüstebach headwater catchment (Germany). This catchment has monitored stream water and associated environmental parameters for over a decade as part of the TERENO initiative. Additionally, there is a paired undisturbed forested catchment that serves as a reference stream. Our approach included a more advanced correlation analysis, namely wavelet analysis, that assists in determining changes in the correlation and lag time between the variables of interest over different time scales. This study found that after deforestation, there was an immediate increase in in-stream DOC concentrations, followed by an increase in nitrate ~1 year later. Overall, the mean DOC concentration increased, and mean nitrate concentration decreased across the catchment post-deforestation. Elevated stream water nutrient levels peaked around 2 to 3 years after the clear-cutting, and returned to pre-deforestation levels after ~5 years. The deforestation had no influence on the anti-correlation between DOC and nitrate. However, the correlation between both compounds and discharge was likely altered due to the increased soil nutrients availability as a result of deforestation. Wavelet coherence analysis revealed the “underlying” changing strengths and directions of the main correlations between DOC, nitrate and discharge on different time scales resulting from severe forest management interventions (here deforestation). This information provides new valuable impact insights for decision making into such forest management interventions.