Biopores and cracks in soils act as fast transport pathways for water and solute, potentially leading to pesticide leaching shortly after application. The biopore module in the agrohydrological model Daisy was developed to simulate preferential water flow directly to drainpipes, in drain-connecting biopores, and to deeper soil layers, in matrix-terminating biopores. We tested the biopore module in Daisy against field measurements of water flow and transport of bentazone and imidacloprid after application to a cracking clay field. We generated two model concepts, drain-connecting biopores (DCB) with drain-connecting biopores and drain-connecting and matrix-terminating biopore (DCMTB) with both drain-connecting and matrix-terminating biopores. Parameters describing the biopores were estimated by inverse modeling of observations of water flow and pesticide concentrations in drains. After calibration, both models satisfactorily simulated water flow and pesticide leaching to drains (root-mean-square error (RMSE)-observations standard deviation ratio (RSR) < 0.1). Particularly, the results showed that the models were able to describe the high concentration of bentazone in drain water shortly after application. Thus, the simpler DCB model preformed just as well or better than the more complex DCMTB model (Delta AIC = 4.68 [AIC, Akaike information criteria]). Discrepancies between observations and simulations in the beginning of the drainage season were attributed to the limitations that arise when simulating dynamic DCB flow paths with a static biopore model. The pesticide distribution in the field over time was well represented, especially by the DCMTB model. We therefore conclude that Daisy can simulate fast breakthrough of pesticides in drain water and describe very well pesticide concentration in drain water throughout the drainage season.