Diffuse sources of pollution like agricultural or urban runoff are important factors in determining the quality of surface waters, although they are more difficult to monitor than point sources. The objective of our study was to verify assumptions that the inflow from agricultural nutrient sources is higher than from urbanized ones. It has been done by comparing the nutrients and organic matter concentrations and loads for three small streams in northern Poland (Pomerania Region). Two streams flowing through agricultural catchments and an urban stream flowing through the city of Gdansk were analysed. Concentrations of nutrients: N-NO${}_{3}^{-}$ N-NH${}_{4}^{+}$, P-PO${}_{4}^{3-}$, total phosphorus, total nitrogen and COD were measured 1–3 times per month in the period from July 2017 to December 2018 in agricultural watersheds and from October 2016 to March 2018 for an urban stream. Seasonal changes in concentrations were analysed with descriptive statistics tools. Principal Component Analysis (PCA) was used to point out the most significant factors determining variations in nutrients and organic matter concentrations with respect to different seasons. The factors included a number of characteristics regarding the catchment and streams: total catchment area, stream length, watershed form ratio, stream slope, flow rate and land use with respect to paved areas, agricultural areas and green areas (parks, forests, meadows and pastures). Although concentrations of nitrogen compounds were higher in streams flowing through agricultural areas, our study showed that total concentrations of phosphorus were higher in the urban stream, especially in summer. In agricultural areas the summer concentrations of nutrients were not high, which was probably due to dense vegetation. The correlation between P-PO${}_{4}^{3-}$ concentration and size of agricultural area in the catchment was observed in winter when no vegetation field cover exists. Our study shows an urgent need to monitor the nutrient loads carried with urban streams especially if discharged into receivers prone to eutrophication.