A novel application of a continuous flow incubation system (CFIS) was used to assess four phosphorus (P) inactivation agents—alum, Phoslock™, a new modified zeolite (Z2G1 or Aqual-P™), and allophone—when used as sediment capping agents to manage internal P loads in lakes. The CFIS technique allowed combined efficacy and sustainability assessment, including: (1) flux measurements during simulation of stratified (anoxic) and mixed (aerobic) conditions on the same sediment through multiple cycles to assess the longevity of a range of product doses; (2) simulation of a summer algal bloom collapse and subsequent burial of the products; and (3) investigation of non-target effects on nitrification and denitrification processes at the sediment–water interface. Minimum P-removal dose rates were found to differ substantially at 80 g m⁻² for alum, 190 g m⁻² for Z2G1, 220 g m⁻² for allophane and 280 g m⁻² for Phoslock™, for similar capping layer thickness of about 2 mm, and would be effective for at least 4 years. All products temporarily suppressed nitrification and denitrification under aerobic conditions, and it may be important to minimise product application to any permanently aerobic zones, such as the littoral areas of a lake. While the aluminium (Al)-based products did not enhance Al fluxes in the CFIS, lanthanum (La) was released at a near constant rate of around 2 mg La m⁻² day⁻¹ from the Phoslock™ treatments over a period of at least 14 days. Spatial variability of sediment P, bioturbation, and burial are factors that will affect up-scaling these results to a whole lake.