Natural fine colloids and nanoparticles have the potential to encapsulate and bind nutrients. Their size and composition is therefore relevant to understand the transport of essential nutrients like phosphorus in an aquatic ecosystem. The aim of this study was to characterize fine colloidal and nanoparticulate bound P of distinct hydromorphological areas in stream water from a forested test site in a small headwater catchment. Asymmetric flow field flow fractionation coupled online to inductively coupled plasma mass spectrometry was applied for size-resolved detection of P, Fe, and Al in the fractions. Online P detection was a challenge due to the low concentrations (in this study down to 0.1 μg/L) in many natural waters. Additionally, the “dissolved” organic matter (DOM) content was derived from the online UV signal. The colloidal P occurred in two size fractions (2–20 and 21–300 nm), which constituted up to 100% of the total river P discharge depending on hydromorphology. For the small size fraction, variations in P concentrations correlated with Al variations; in addition, a high Fe presence in both fractions was accompanied by high P concentrations. Moreover, DOM was detected with P in the presence of Fe and Al, suggesting that Fe and Al are carriers of P and associated with organic matter. The developed methodology enables the inputs and source regions of fine colloidal and nanoparticulate fractions within a small river of a headwater catchment to be traced and conceptually defined for the first time.