Reducing the discharge of contaminants present in runoff water is important for a clean environment. This paper analyses field test results of three pilot-scale horizontal runoff water treatment zones filled with mixtures of zero valent iron (ZVI), activated carbon (AC), silica spongolite (SS), zeolite (Z), and limestone (LS). The investigated systems were (S1) ZVI/AC/SS, (S2) ZVI/AC/Z and (S3) ZVI/AC/LS. The efficiency of the three systems in the removal of Cd, Cu, Ni, Pb, Zn, COD and ammonium ions from runoff water was compared and the factors (temperature, pH, redox potential, hydraulic conductivity) and relationships affecting treatment effectiveness were determined. A statistical analysis of effluent contaminant concentrations and physicochemical parameters of effluent solutions included descriptive statistics, analysis of variance (ANOVA), a multidimensional analysis using a Principal Component Analysis (PCA), a factor analysis (FA) and a cluster analysis (CA). The ANOVA and cluster analyses indicated similarities between systems containing SS and LS. As a consequence, using cheaper SS can reduce investment costs. In addition, there were no significant differences between the three systems regarding Cd and Ni removal, while Cu and Pb were removed to almost 100%. The results indicate that all the tested materials supported ZVI and AC in the removal of heavy metals in a similar way. However, runoff water was enriched with nitrogen oxides and sulfates while flowing through treatment zones with SS and LS. The enrichment increased with increasing temperature and redox potential. The conducted analyses indicate that the most suitable mixture is ZVI/AC/Z. It should be emphasized that the ongoing processes (precipitation and ZVI corrosion) reduced the hydraulic conductivity of the filters up to two orders of magnitude. Expansive iron corrosion was the most limiting factor in ZVI filtration systems. In the future, applications decreasing the percentage of ZVI in the mixture are suggested.