Contaminant transport in the subsurface is generally affected by a large number of nonlinear and often interactive physical, chemical and biological processes. Simulating these processes requires a coupled reactive transport code that integrates the physical processes of water flow and advective-dispersive transport with a range of biogeochemical processes. In this presentation we summarize three recently developed coupled biogeochemical models that are all based on the HYDRUS software packages for variably saturated flow and transport. One model resulted from coupling HYDRUS with the UNSATCHEM module. While restricted to major ion chemistry, this program enables quantitative predictions of such problems as analyzing the effects of salinity on plant growth and the amount of water and amendment required to reclaim salt-affected soil profiles. The second model, HP1, resulted from coupling HYDRUS with the PHREEQC biogeochemical code. This programs accounts for a wide range of instantaneous or kinetic chemical and biological reactions, including complexation, cation exchange, surface complexation, precipitation-dissolution and/or redox reactions. The versatility of HP1 is demonstrated on an example involving the transport of toxic trace elements in the subsurface. The third model resulted from coupling a multi-component reactive transport module CW2D (Constructed Wetlands 2D) with HYDRUS-2D. CW2D was developed to model the biochemical transformation and degradation processes in subsurface-flow constructed wetlands and it considers the biochemical degradation and transformation processes for organic matter, nitrogen and phosphorus. Monod-type expressions are used to describe the process rates. The biochemical components defined in CW2D include dissolved oxygen, three fractions of organic matter (readily- and slowly-biodegradable, and inert), four nitrogen compounds (ammonium, nitrite, nitrate, and dinitrogen), inorganic phosphorus, and heterotrophic and autotrophic micro-organisms. Heterotrophic bacteria are assumed to be responsible for hydrolysis, mineralization of organic matter (aerobic growth) and denitrification (anoxic growth). Autotrophic bacteria are assumed to be responsible for nitrification.