The efficiency and mechanism of orthophosphate—soluble reactive phosphorus (SRP)—inactivation in eutrophic lakes using controlled resuspension and calcite application into the sediment were investigated in this study. Two calcite materials, industrially produced precipitated calcium carbonate (PCC) and natural ground limestone (GCC), were tested in short-term batch experiments and long-term sediment incubations under oxic and anoxic conditions. Maximum SRP adsorption capacity calculated using Langmuir model for PCC (3.11 mg PO43− g−1) was 6 times higher than of GCC (0.43 mg PO43− g−1), reflecting substantial difference in the surface area of calcite materials (12.36 and 1.72 m2 g−1, respectively). PCC applied into the sediment during controlled resuspension reduced SRP release by 95% (oxic) and 78% (anoxic incubation) at medium dose (0.75 kg m−2) and suppressed it completely at high dose (1.5 kg m−2) for at least 3 months, irrespectively of incubation conditions. The maximum achieved reduction of SRP release using GCC was also meaningful: 78% under oxic and 56% under anoxic conditions, but this required very high doses of this material (6 kg m−2). Mechanisms of SRP inactivation by calcites were: (1) adsorption of SRP during application into the resuspended sediment and (2) precipitation of calcium-phosphate compounds (Ca-PO4) during subsequent incubation, which was reflected in a substantial increase in the HCl-P fraction (phosphorus extractable in 0.5 M HCl) in sediments enriched with calcite, irrespectively of oxygen presence. However, anoxia strongly promoted the formation of this fraction: the rise of HCl-P was 2–6 times higher in anoxic than in oxic conditions, depending on the dose and form of calcite applied. The results showed that SRP inactivation using the controlled resuspension method is only successful if highly efficient reactive materials are used, due to large amount of SRP being released from sediment during resuspension. Thus, calcite materials exhibiting high adsorption capacity should be used in this lakes’ restoration technology to ensure fast and sufficient SRP inactivation. The rise in the HCl-P fraction in sediment suggests SRP inactivation through precipitation of relatively stable Ca-PO4 minerals, which makes calcite a suitable agent for sustainable, long term SRP inactivation. As anoxic conditions promoted formation of these compounds, calcite seems to be a promising SRP inactivation agent in highly reductive sediments.