This study aimed to investigate the effects of flow rate, initial soil moisture conditions and vermicompost (VC) application on total dissolved solids (TDS), nitrate (NO3), dissolved organic carbon (DOC) and colloid leaching from soil. Columns were filled with natural soil or VC-amended soil and were leached under unsaturated flow conditions using flow rates of 4.3–5.1, 2.5 and 0.4 mL/min. Two sets of experiments were conducted, one with the soils at initial air-dried conditions and the other with initial saturated conditions. Control experiments were conducted under saturated-flow conditions using flow rates of 2.7–3.8 mL/min for comparison. Results of the leaching experiments showed that EC, nitrate and DOC levels in the effluent were higher for the VC-amended soil versus the un-amended soil. Leaching under initial air-dried conditions and at the lowest flow rate (lowest water saturation) also produced higher EC, nitrate and DOC concentrations in the effluent. Conversely, effluent colloid concentrations were slightly higher for saturated-flow conditions, and elution behavior was similar between the un-amended and VC-amended soils. Statistical analysis revealed that the total leaching of TDS, nitrate, DOC and colloid under the initial air-dried conditions was not significantly different (p < 0.05) in comparison with the initial saturated conditions. Although, higher flow rates showed high amount of total leaching of TDS, nitrate, DOC and colloid, unsaturated flow rate of 2.5 mL/min leached more efficiently than flow rate of 2.7–4.3 mL/min in un-amended soil. Findings of this study would help decision makers to better manage soil salinity, drainage and groundwater pollution. Particularly, applying lower flow rates for irrigation applications to maintain unsaturated conditions can significantly decrease colloid migration and soil erosion.