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Application of biochar to agricultural fields to improve soil quality has increased in popularity in recent years, but limited attention is generally paid to existing field conditions before biochar application. This study examined the short-term physicochemical effects of biochar amendment in an agricultural field in Denmark with a calcium carbonate (CaCO3) gradient. The field comprised four reference plots and four plots to which biochar (birch wood pyrolyzed at 500°C) was applied at a rate of 20 t ha−1. Five undisturbed soil columns (10 cm diam., 8 cm height) were sampled from each plot 7 mo after biochar application, and a series of leaching experiments was conducted. The leachate was analyzed for tritium (used as a tracer), colloids, and phosphorus concentration. The results revealed that the presence of CaCO3 has resulted in marked changes in soil structure (bulk density) and soil chemical properties (e.g., pH and ionic strength), which significantly affected air and water transport and colloid and phosphorous leaching. In denser soils (bulk density, 1.57–1.69 g cm−3) preferential flow dominated the transport and caused an enhanced movement of air and water, whereas in less dense soils (bulk density, 1.38–1.52 g cm−3) matrix flow predominated the transport. Compared with reference soils, biochar-amended soils showed slightly lower air permeability and a shorter travel time for 5% of the applied tracer (tritium) to leach through the soil columns. Colloid and phosphorus leaching was observed to be time dependent in soils with low CaCO3. Biochar-amended soils showed higher colloid and P release than reference soils. Field-scale variations in total colloid and P leaching reflected clear effects of changes in pH and ionic strength due to the presence of CaCO3. There was a linear relationship between colloid and P concentrations in the leachate, suggesting that colloid-facilitated P leaching was the dominant P transport mechanism.