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. Multicomponent solute transport models can be divided into two broad groups: general models and models with specific chemistry. Models with specific chemistry are generally restricted to certain prescribed chemical systems and thus are generally constrained to very specific applications. However, they are often much easier to use and computationally much more efficient than general models. Models simulating the transport of major ions and various reclamation models are typical examples of models with specified chemistry. These models typically consider the transport of major ions and their mutual reactions such as complexation, cation exchange, and precipitation/dissolution. Models with specific chemistry often also includes those simulating carbon and nitrogen cycles, which are increasingly becoming a standard feature of many environmental models. On the other hand, models with generalized chemistry provide users with much more freedom in designing particular chemical systems, and thus also permit a much broader range of applications. Users then either can select species and reactions from large geochemical databases, or are able to define their own species with particular chemical properties and reactions. In this presentation we summarize three recently developed coupled biogeochemical models (HP1, HYDRUS-1D, and CW2D) that are all based on the HYDRUS software packages for variably saturated flow and transport. Of these HP1 is a typical example of a model with generalized chemistry, while the HYDRUS-1D model with the major ion chemistry module and CW2D represent examples of models with specific chemistry. Description of each model and typical examples will be presented. The first 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. Possible applications of HP1 involve a) the transport of heavy metals (Zn²⁺, Pb²⁺, and Cd²⁺) subject to multiple cation exchange reactions, b) transport with mineral dissolution of amorphous SiO₂ and gibbsite (Al(OH) ₃), c) heavy metal transport in a medium with a pH-dependent cation exchange complex, d) infiltration of a hyperalkaline solution in a clay sample (this example considers kinetic precipitation-dissolution of kaolinite, illite, quartz, calcite, dolomite, gypsum, hydrotalcite, and sepiolite), e) long-term transient flow and transport of major cations (Na⁺, K⁺, Ca²⁺, and Mg²⁺) and heavy metals (Cd²⁺, Zn²⁺, and Pb²⁺) in a soil profile, f) cadmium leaching in acid sandy soils, g) radionuclide transport, h) long term uranium migration in agricultural field soils following mineral P-fertilization, and i) the fate and subsurface transport of explosives (TNT). The second model resulted from coupling HYDRUS with the UNSATCHEM geochemical 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. We will present an application of HYDRUS-1D to analyze water flow and solute transport (SAR, ESP, EC, and concentration of individual cations) in three soil lysimeters that were used to evaluate salinisation and alkalisation hazards in a soil irrigated with waters of different quality. 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.