To optimize the workflow of civil engineering construction in a harbour, this paper developed a framework of the contaminant leaching assessment carried out on the stabilized/solidified dredged soil material. The specimens included the sampled sediments collected from the in situ fieldwork in Arendal and Kongshavn. The background levels of the concentration of pollutants were evaluated to assess the cumulative surface leaching of substances from samples over two months. The contamination of soil was assessed using a structured workflow scheme on the following toxic substances, heavy metals—As, Pb, Cd, Cr, Hg, Ni, and Zn; organic compounds—PAH-16 and PCB; and organotin compounds—TBT. The numerical computation and data analysis were applied to the results of geochemical testing creating computerised solutions to soil quality evaluation in civil engineering. Data modelling enabled the estimation of leaching of the contaminants in one year. The estimated leaching of As is 0.9153 mg/m2, for Ni—2.8178 mg/m2, for total PAH-16 as 0.0507 mg/m2, and for TBT—0.00061 mg/m2 per year. The performance of the sediments was examined with regard to permeability through a series of the controlled experiments. The environmental engineering tests were implemented in the Swedish Geotechnical Institute (SGI) in a triplicate mode over 64 days. The results were compared for several sites and showed that the amount of As is slightly higher in Kongshavn than for Arendal, while the content of Cd, Cr, and Ni is lower. For TBT, the levels are significantly lower than for those at Arendal. The algorithm of permeability tests evaluated the safety of foundation soil for construction of embankments and structures. The optimized assessment methods were applied for monitoring coastal areas through the evaluated permeability of soil and estimated leaching rates of heavy metals, PHB, PACs, and TBT in selected test sites in harbours of southern Norway.