Reactive transport models are essential tools for predicting contaminant fate and transport in the subsurface and for designing effective remediation strategies. Sound understanding of subsurface mixing in heterogeneous porous media is the key for the realistic modeling of reactive transport. This dissertation aims to investigate the extent of mixing and improve upscaling effective macroscopic models for mixing-controlled reactive transport in connected heterogeneous formations, which usually exhibit strongly anomalous transport behavior. In this research, a novel approach is developed for an accurate geostatistical characterization of connected heterogeneous formations transformed from Gaussian random fields. Numerical experiments are conducted in such heterogeneous fields with different connectivity to investigate the performance of macroscopic mean transport models for simulating mixing-controlled reactive transport. Results show that good characterization of anomalous transport of a conservative tracer does not necessarily mean that the models may characterize mixing well and that, consequently, it is questionable that the models capable of characterizing anomalous transport behavior of a conservative tracer are appropriate for simulating mixing-controlled reactive transport. In connected heterogeneous fields with large hydraulic conductivity variances, macroscopic mean models ignoring concentration variations yield good prediction, while in fields with intermediate conductivity variances, the models must consider both the mean concentration and concentration variations, which are very difficult to evaluate both theoretically and experimentally. An innovative and practical approach is developed by combining mean conservative and reactive breakthrough curves for estimating concentration variations, which can be subsequently used by variance transport models for prediction. Furthermore, a new macroscopic framework based on the dual-permeability conceptualization is developed for describing both mean and concentration variation for mixing-controlled reactive transport. The developed approach and models are validated by numerical and laboratory visualization experiments. In particular, the new dual-permeability model demonstrates significant improvement for simulating mixing-controlled reactive transport in heterogeneous media with intermediate conductivity variances. Overall, results, approaches and models from this dissertation advance the understanding of subsurface mixing in anomalous transport and significantly improve the predictive ability for modeling mixing-controlled reactive transport in connected heterogeneous media.