Using industrial by-products (IBPs) in conjunction with vegetated buffer strips (VBSs) has the potential to be a cost-effective strategy for tackling phosphorus (P) export from agricultural land. Using an integrated mesocosm approach, we examined the effect of surface application of IBPs within VBSs on the removal of P fractions in surface and sub-surface flow. Artificial run-off was applied to VBSs (1.2 m long × 0.4 m wide, and 5% slope) that were amended with either 20 t ha−1 of Al-based water treatment residual (Al-WTR) or 20 t ha−1 of ochre, or remained as unamended controls. To explore the persistence of the effects of amendment over multiple run-off events, two 30-minute artificial run-off events (3 litre minute−1) were applied to the mesocosms over a period of five days. When compared with inflow concentrations, the unamended VBSs reduced total P (37–54%) and particulate P (61–64%) concentrations in surface run-off, but increased soluble reactive P (SRP) (5–9%) and total dissolved P concentrations (4–8%). Enhancing VBSs with IBPs improved retention of soluble P fractions in surface run-off, for example, 61–62 and 15–19% of the SRP in the inflow was retained in VBSs amended with Al-WTR and ochre, respectively. Surface application of either ochre or Al-WTR also reduced the concentrations of soluble P fractions in sub-surface flow. The magnitude of these effects depended on inflow P concentrations. Unlike Al-WTR, the effectiveness of ochre gradually declined over the duration of each run-off event because of erosion of ochre by run-off.